Compositions and methods for the detection, diagnosis and therapy of hematological malignancies

ABSTRACT

Disclosed are methods and compositions for the detection, diagnosis, prognosis, and therapy of hematological malignancies, and in particular, B cell leukemias, lymphomas and multiple myelomas. Disclosed are compositions, methods and kits for eliciting immune and T cell responses to specific malignancy-related antigenic polypeptides and antigenic polypeptide fragments thereof in an animal. Also disclosed are compositions and methods for use in the identification of cells and biological samples containing one or more hematological malignancy-related compositions, and methods for the detection and diagnosis of such diseases and affected cell types. Also disclosed are diagnostic and therapeutic kits, as well as methods for the diagnosis, therapy and/or prevention of a variety of leukemias and lymphomas.

CROSS-REFERENCES TO RELATED APPLICATIONS

[0001] This application is a continuation in part of U.S. Ser. No.09/796,692 filed Mar. 1, 2001, which claims priority to U.S. ProvisionalPatent Application Serial No. 60/186,126, filed Mar. 1, 2000; Serial No.60/190,479, filed Mar. 17, 2000; Serial No. 60/200,545, filed Apr. 27,2000; Serial No. 60/200,303, filed Apr. 28, 2000; Serial No. 60/200,779,filed Apr. 28, 2000; Serial No. 60/200,999; filed May 1, 2000; SerialNo. 60/202,084, filed May 4, 2000; Serial No. 60/206,201, filed May 22,2000; Serial No. 60/218,950, filed Jul. 14, 2000; Serial No. 60/222,903,filed Aug. 3, 2000; Serial No. 60/223,416, filed Aug. 4, 2000; andSerial No. 60/223,378, filed Aug. 7, 2000; the entire specification,claims, sequences and figures of each of which is specificallyincorporated herein by reference in its entirety without disclaimer andfor all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

[0002] NOT APPLICABLE

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAMLISTING APPENDIX SUBMITTED ON A COMPACT DISK

[0003] The Sequence Listing written in file—135-2.APP, 6,436,297 bytes,created on Jun. 18, 2002 on duplicate copies of compact disc of thewritten form of the Sequence Listing, i.e., “Copy 1 of 3” and “Copy 2 of3”, and the sequence information recorded in computer readable form oncompact disc, i.e., “Copy 3 of 3” for application Ser. No. 10/040,862,Gaiger et al., COMPOSITIONS AND METHODS FOR THE DETECTION, DIAGNOSIS ANDTHERAPY OF HEMATOLOGICAL MALIGNANCIES, is hereby incorporated byreference.

1. BACKGROUND OF THE INVENTION

[0004] 1.1 Field of the Invention

[0005] The present invention relates generally to the fields of cancerdiagnosis and therapy. More particularly, it concerns the surprisingdiscovery of compositions and methods for the detection andimmunotherapy of hematological malignancies, and particularly, B cellleukemias, and lymphomas and multiple myelomas. The invention providesnew, effective methods, compositions and kits for eliciting immune andT-cell response to antigenic polypeptides, and antigenic peptidefragments isolated therefrom, and methods for the use of suchcompositions for diagnosis, detection, treatment, monitoring, and/orprevention of various types of human hematological malignancies. Inparticular, the invention provides polypeptide, peptide, antibody,antigen binding fragment, hybridoma, host cell, vector, andpolynucleotide compounds and compositions for use in identification anddiscrimination between various types of hematological malignancies, andmethods for the detection, diagnosis, prognosis, monitoring, and therapyof such conditions in an affected animal.

[0006] 1.2 Description of Related Art

[0007] 1.2.1 Hematological Malignancies

[0008] Hematological malignancies, such as leukemias and lymphomas, areconditions characterized by abnormal growth and maturation ofhematopoietic cells. Leukemias are generally neoplastic disorders ofhematopoietic stem cells, and include adult and pediatric acute myeloidleukemia (AML), chronic myeloid leukemia (CML), acute lymphocyticleukemia (ALL), chronic lymphocytic leukemia (CLL) and secondaryleukemia. Among lymphomas, there are two distinct groups: non-Hodgkin'slymphoma (NHL) and Hodgkin's disease. NHLs are the result of a clonalexpansion of B- or T-cells, but the molecular pathogenesis of Hodgkin'sdisease, including lineage derivation and clonality, remains obscure.Other hematological malignancies include myelodysplastic syndromes(MDS), myeloproliferative syndromes (MPS) and myeloma. Hematologicalmalignancies are generally serious disorders, resulting in a variety ofsymptoms, including bone marrow failure and organ failure.

[0009] NHLs are the sixth most common cause of cancer related deaths inthe United States. Only prostate, breast, lung, colorectal and bladdercancer currently exceed lymphoma in annual incidence. In 1995, more than45,000 new NHLs were diagnosed, and over 21,000 patients died of thesediseases. The average age of lymphoma patients is relatively young (42years), and the resulting number of years of life lost to these diseasesrenders NHLs fourth in economic impact among cancers in the UnitedStates. In the past 15 years, the American Cancer Society reported a 50%increase in the incidence of NHLs, one of the largest increases for anycancer group. Much of this increase has been attributed to thedevelopment of lymphomas in younger men who have acquired AIDS.Lymphomas are also the third most common childhood malignancy andaccount for approximately 10% of cancers in children. The survival rate(all ages) varies from 73% (low risk) to 26% (high risk).

[0010] 1.3 Deficiencies in the Prior Art

[0011] Treatment for many hematological malignancies, includingleukemias and lymphomas, remains difficult, and existing therapies arenot universally effective. While treatments involving specificimmunotherapy appear to have considerable potential, such treatmentshave been limited by the small number of known malignancy-associatedantigens. Moreover the ability to detect such hematological malignanciesin their early stages can be quite difficult depending upon theparticular malady. The lack of a sufficient number of specificdiagnostic and prognostic markers of the diseases, and identification ofcells and tissues that can be affected, has significantly limited thefield of oncology.

[0012] Accordingly, there remains a need in the art for improved methodsfor detecting, screening, diagnosis and treatment of hematologicalmalignancies such as B cell leukemias and lymphomas and multiplemyelomas. The present invention fulfills these and other inherent needsin the field, and provides significant advantages in the detection ofcells, and cell types that express one or more polypeptides that havebeen shown to be over-expressed in one or more of such hematologicalmalignancies.

2. SUMMARY OF THE INVENTION

[0013] The present invention addresses the foregoing long-felt need andother deficiencies in the art by identifying new and effectivestrategies for the identification, detection, screening, diagnosis,prognosis, prophylaxis, therapy, and immunomodulation of one or morehematological malignancies, and in particular, B cell leukemias andlymphomas, and multiple myelomas.

[0014] The present invention is based, in part, upon the surprising andunexpected discovery that certain previously unknown or unidentifiedhuman polypeptides, peptides, and antigenic fragments derived therefromhave now been identified that are overexpressed in one or more types ofhematological malignancies. The genes encoding several of thesepolypeptides are now identified and obtained in isolated form, and havebeen characterized using a series of molecular biology methodologiesincluding subtractive library analysis, microarray screening,polynucleotide sequencing, peptide and epitopic identification andcharacterization, as well as expression profiling, and in vitro wholegene cell priming. A set of these polynucleotides, and the polypeptides,peptides, and antigenic fragments they encode are now identified andimplicated in the complex processes of hematological malignancy diseaseonset, progression, and/or outcome, and in particular, diseases such asleukemias and lymphomas.

[0015] The inventors have further demonstrated that a number of thesepolynucleotides, and their encoded polypeptides, as well as antibodies,antigen presenting cells, T cells, and the antigen binding fragmentsderived from such antibodies are useful in the development ofparticularly advantageous compositions and methods for the detection,diagnosis, prognosis, prophylaxis and/or therapy of one or more of thesediseases, and particularly those conditions that are characterized by(a) an increased, altered, elevated, or sustained expression of one ormore polynucleotides that comprise at least a first sequence region thatcomprises a nucleic acid sequence as disclosed in any one of SEQ IDNO:9598 through SEQ ID NO:9610 or (b) an increased, altered, elevated,or sustained biological activity of one or more polypeptides thatcomprise at least a first sequence region that comprises an amino acidsequence as disclosed in any one of SEQ ID NO:9611 through SEQ IDNO:10466.

[0016] The present invention also provides methods and uses for one ormore of the disclosed peptide, polypeptide, antibody, antigen bindingfragment, and polynucleotide compositions of the present invention ingenerating an immune response or in generating a T-cell response in ananimal, and in particular in a mammal such as a human. The inventionalso provides methods and uses for one or more of these compositions inthe identification, detection, and quantitation of hematologicalmalignancy compositions in clinical samples, isolated cells, wholetissues, and even affected individuals. The compositions and methodsdisclosed herein also may be used in the preparation of one or morediagnostic reagents, assays, medicaments, or therapeutics, for diagnosisand/or therapy of such diseases.

[0017] In a first important embodiment, there is provided a compositioncomprising at least a first isolated peptide or polypeptide thatcomprises an amino acid sequence that is at least about 80%, about 81%,about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%,about 95%, about 96%, about 97%, about 98%, or about 99% identical tothe amino acid sequence of any one of SEQ ID NO:9611 to SEQ ID NO:10466.Exemplary preferred sequences are those that comprise at least a firstcoding region that comprises an amino acid sequence that is at leastabout 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about91%, about 92%, about 93%, or about 94% identical to the amino acidsequence of any one of SEQ ID NO:9611 to SEQ ID NO:10466, with thosesequences that comprise at least a first coding region that comprises anamino acid sequence that is at least about 95%, about 96%, about 97%,about 98%, or about 99% identical to the amino acid sequence of any oneof SEQ ID NO:9611 to SEQ ID NO:10466 being examples of particularlypreferred sequences in the practice of the present invention. Likewise,peptide and polypeptide compounds and compositions are also providedthat comprise, consist essentially of, or consist of the amino acidsequence of any one of SEQ ID NO:9611 to SEQ ID NO:10466.

[0018] In a similar fashion, there are also embodiments disclosed hereinthat provide compositions and methods for the detection, diagnosis,prognosis, prophylaxis, treatment, and therapy of B cell leukemia,lymphoma and multiple myeloma. Exemplary preferred peptide andpolypeptide compounds and compositions relating to this aspect of theinvention include, but are not limited to, those peptide and polypeptidecompounds or compositions that comprise at least a first isolatedpeptide or polypeptide that comprises an amino acid sequence that is atleast about 80%, about 81%, about 82%, about 83%, about 84%, about 85%,about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%,or about 99% identical to the amino acid sequence of any one of SEQ IDNO:9611 to SEQ ID NO:10466, and those that comprise at least a firstcoding region that comprises an amino acid sequence that is at leastabout 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about91%, about 92%, about 93%, or about 94% identical to the amino acidsequence of any one of SEQ ID NO:9611 to SEQ ID NO:10466, and even thosesequences that comprise at least a first coding region that comprises anamino acid sequence that is at least about 95%, about 96%, about 97%,about 98%, or about 99% identical to the amino acid sequence of any oneof SEQ ID NO:9611 to SEQ ID NO:10466.

[0019] Exemplary peptides of the present invention may be of anysuitable length, depending upon the particular application thereof, andencompass those peptides that are about 9, about 10, about 15, about 20,about 25, about 30, about 35, about 40, about 45, about 50, about 55,about 60, about 65, about 70, about 75, about 80, about 85, about 90,about 95, or about 100 or so amino acids in length. Of course, thepeptides of the invention may also encompass any intermediate lengths orintegers within the stated ranges.

[0020] Exemplary polypeptides and proteins of the present invention maybe of any suitable length, depending upon the particular applicationthereof, and encompass those polypeptides and proteins that are about100, about 150, about 200, about 250, about 300, about 350, or about 400or so amino acids in length. Of course, the polypeptides and proteins ofthe invention may also encompass any intermediate lengths or integerswithin the stated ranges.

[0021] The peptides, polypeptides, proteins, antibodies, and antigenbinding fragments of the present invention will preferably comprise asequence of at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55,60, 65, 70, 75, 80, 85, 90, 95 or 100 contiguous amino acids from anyone of SEQ ID NO:9611 to SEQ ID NO:10466.

[0022] Furthermore, the polypeptides, proteins, antibodies, and antigenbinding fragments of the present invention will even more preferablycomprise at least a first isolated coding region that comprises asequence of at least about 100, 110, 120, 130, 140, 150, 160, 170, 180,190, or 200 contiguous amino acids from any one of SEQ ID NO:9611 to SEQID NO:10466.

[0023] Likewise, the polypeptides, proteins, antibodies, and antigenbinding fragments of the present invention may comprise at least a firstisolated coding region that comprises a substantially longer sequence,such as for example, one of at least about 200, 220, 240, 260, 280, or300 or more contiguous amino acids from any one of SEQ ID NO:9611 to SEQID NO:10466.

[0024] In illustrative embodiments, and particularly in thoseembodiments concerning methods and compositions relating to B cellleukemias, lymphomas and multiple myelomas, the polypeptides of theinvention comprise an amino acid sequence that (a) comprises, (b)consists essentially of, or (c) consists of, the amino acid sequence ofSEQ ID NO:9611 to SEQ ID NO:10466.

[0025] The polypeptides and proteins of the invention preferablycomprise an amino acid sequence that is encoded by at least a firstnucleic acid segment that comprises an at least 21, 22, 23, 24, 25, 26,27, 28, 29, or 30 contiguous nucleotide sequence of any one of SEQ IDNO:9598 to SEQ ID NO:9610.

[0026] The polypeptides and proteins of the invention may alsopreferably comprise an amino acid sequence encoded by at least a firstnucleic acid segment that comprises an at least about 31, 32, 33, 34,35, 36, 37, 38, 39, or 40 contiguous nucleotide sequence of any one ofSEQ ID NO:9598 to SEQ ID NO:9610. The polypeptides and proteins of theinvention may also preferably comprise one or more coding regions thatcomprise an amino acid sequence encoded by at least a first nucleic acidsegment that comprises an at least about 41, 42, 43, 44, 45, 46, 47, 48,49, or 50 contiguous nucleotide sequence of any one of SEQ ID NO:9598 toSEQ ID NO:9610. The polypeptides and proteins of the invention may alsopreferably comprise one or more coding regions that comprise an aminoacid sequence encoded by at least a first nucleic acid segment thatcomprises an at least about 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60contiguous nucleotide sequence of any one of SEQ ID NO:9698 to SEQ IDNO:9610. The polypeptides and proteins of the invention may alsopreferably comprise one or more coding regions that comprise an aminoacid sequence encoded by at least a first nucleic acid segment thatcomprises an at least about 70, 80, 90, 100, 110, 120, 130, 140 or 150contiguous nucleotide sequence of any one of SEQ ID NO:9598 to SEQ IDNO:9610. The polypeptides and proteins of the invention may alsopreferably comprise one or more coding regions that comprise an aminoacid sequence encoded by at least a first nucleic acid segment thatcomprises an at least about 175, 200, 225, 250, 275, 300, 325, 350, 375,or 400 contiguous nucleotide sequence of any one of SEQ ID NO:9598 toSEQ ID NO:9610. The polypeptides and proteins of the invention may alsopreferably comprise one or more coding regions that comprise an aminoacid sequence encoded by at least a first nucleic acid segment thatcomprises an at least about 500, 600, 700, 800, 900, 1000, 1100, 1200,1300, 1400, or 1500 contiguous nucleotide sequence of any one of SEQ IDNO:9598 to SEQ ID NO:9610.

[0027] In a second important embodiment, there is provided a compositioncomprising at least a first isolated polynucleotide that comprises anucleic acid sequence that is at least about 80%, about 81%, about 82%,about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%,about 96%, about 97%, about 98%, or about 99% identical to the nucleicacid sequence of any one of SEQ ID NO:9598 to SEQ ID NO:9610. Exemplarypreferred sequences are those that comprise a nucleic acid sequence thatis at least about 85%, about 86%, about 87%, about 88%, about 89%, about90%, about 91%, about 92%, about 93%, or about 94% identical to thenucleic acid sequence of any one of SEQ ID NO:9598 to SEQ ID NO:9610,with those sequences that comprise at least a nucleic acid sequence thatis at least about 95%, about 96%, about 97%, about 98%, or about 99%identical to the nucleic acid sequence of any one of SEQ ID NO:9598 toSEQ ID NO:9610 being examples of particularly preferred sequences in thepractice of the present invention.

[0028] In embodiments that relate particularly to compositions andmethods for the detection, diagnosis, prognosis, prophylaxis, treatment,and therapy of B cell leukemias, lymphomas, and multiple myelomasexemplary preferred polynucleotide compositions include thosecompositions that comprise at least a first isolated nucleic acidsegment that comprises a sequence that is at least about 80%, about 81%,about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%,about 95%, about 96%, about 97%, about 98%, or about 99% identical tothe nucleic acid sequence of any one of SEQ ID NO:9598 to SEQ IDNO:9610. Such polynucleotides will preferably comprise one or moreisolated coding region, each of which may (a) comprise, (b) consistessentially of, or (c) consist of, the nucleic acid sequence of SEQ IDNO:9598 to SEQ ID NO:9610.

[0029] Exemplary polynucleotides of the present invention may be of anysuitable length, depending upon the particular application thereof, andencompass those polynucleotides that (a) are at least about, or (b)comprise at least a first isolated nucleic acid segment that is at leastabout 27, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 120, 140, 150, 160,170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300,320, 340, 360, 380, 400, 420, 440, 460, 480, 500, 520, 540, 560, 580,600, 625, 650, 675, 700, 750, 800, 850, 900, 950, or 1000 or so nucleicacids in length, as well as longer polynucleotides that (a) are at leastabout, or (b) comprise at least a first isolated nucleic acid segmentthat is at least about 1000, 1025, 1050, 1075, 1100, 150, 1200, 1250,1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850,1900, 1950, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900,or 3000 or so nucleic acids in length, as well as substantially largerpolynucleotides. Of course, the polynucleotides and nucleic acidsegments of the invention may also encompass any intermediate lengths orintegers within the stated ranges.

[0030] The compositions of the present invention may comprise a singlepolypeptide or polynucleotide, or alternatively, may comprise two ormore such hematological malignancy compounds, such as for example, twoor more polypeptides, two or more polynucleotides, or even combinationsof one or more peptides or polypeptides, along with one or morepolynucleotides. When two or more polypeptides are contemplated forparticular applications, the second and/or third and/or fourth, etc.isolated peptides and/or polypeptides will preferably comprise an aminoacid sequence that is at least about 91%, 93%, 95%, 97%, or 99%identical to the amino acid sequence of any one of SEQ ID NO:9611 to SEQID NO:10466. Alternatively, the polynucleotides of the invention maycomprise one or more coding regions that encode a first fusion proteinor peptide, such as an adjuvant-coding region fused in correct readingframe to one or more of the disclosed hematological malignancy peptidesor polypeptides. Alternatively, the fusion protein may comprise ahematological malignancy polypeptide or peptide fused, in correctreading frame, to a detectable protein or peptide, or to animmunostimulant protein or peptide, or other such construct. Fusionproteins such as these are particularly useful in those embodimentsrelating to diagnosis, detection, and therapy of one or more of thehematological malignancies as discussed herein.

[0031] The invention also provides a composition comprising at least afirst hybridoma cell line that produces a monoclonal antibody havingimmunospecificity for one or more of the peptides or polypeptides asdisclosed herein, or at least a first monoclonal antibody, or anantigen-binding fragment thereof, that has immunospecificity for such apeptide or polypeptide. The antigen binding fragments may comprise alight chain variable region, a heavy-chain variable region, a Fabfragment, a F(ab)₂ fragment, an Fv fragment, an scFv fragment, or anantigen-binding fragment of such an antibody.

[0032] The invention also provides a composition comprising at least afirst isolated antigen-presenting cell that expresses a peptide orpolypeptide as disclosed herein, or a plurality of isolated T cells thatspecifically react with such a peptide or polypeptide. Such pluralitiesof isolated T cells may be stimulated or expanded by contacting the Tcells with one or more peptides or polypeptides as described herein. TheT cells may be cloned prior to expansion, and may be obtained from bonemarrow, a bone marrow fraction, peripheral blood, or a peripheral bloodfraction from a healthy mammal, or from a mammal that is afflicted withat least a first hematological malignancy such as leukemia or lymphoma.

[0033] As described above, the isolated polypeptides of the inventionmay be on the order of from 9 to about 1000 amino acids in length, oralternatively, may be on the order of from 50 to about 900 amino acidsin length, from 75 to about 800 amino acids in length, from 100 to about700 amino acids in length, or from 125 to about 600 amino acids inlength, or any other such suitable range.

[0034] The isolated nucleic acid segments that encode such isolatedpolypeptides may be on the order of from 27 to about 10,000 nucleotidesin length, from 150 to about 8000 nucleotides in length, from 250 toabout 6000 nucleotides in length, from 350 to about 4000 nucleotides inlength, or from 450 to about 2000 nucleotides in length, or any othersuch suitable range.

[0035] The nucleic acid segment may be operably positioned under thecontrol of at least a first heterologous, recombinant promoter, such asa tissue-specific, cell-specific, inducible, or otherwise regulatedpromoter. Such promoters may be further controlled or regulated by thepresence of one or more additional enhancers or regulatory regionsdepending upon the particular cell type in which expression of thepolynucleotide is desired. The polynucleotides and nucleic acid segmentsof the invention may also be comprised within a vector, such as aplasmid, or viral vector. The polypeptides and polynucleotides of theinvention may also be comprised within a host cell, such as arecombinant host cell, or a human host cell such as a blood or bonemarrow cell.

[0036] The polynucleotides of the invention may comprise at least afirst isolated nucleic acid segment operably attached, in frame, to atleast a second isolated nucleic acid segment, such that thepolynucleotide encodes a fusion protein in which the first peptide orpolypeptide is linked to the second peptide or polypeptide.

[0037] The polypeptides of the present invention may comprise acontiguous amino acid of any suitable length, such as for example, thoseof about 2000, about 1900, about 1850, about 1800, about 1750, about1700, about 1650, about 1600, about 1550, about 1500, about 1450, about1400, about 1350, about 1300, about 1250, about 1200, about 1150, about1100 amino acids, or about 1000 or so amino acids in length. Likewise,the polypeptides and peptides of the present invention may compriseslightly shorter contiguous amino acid coding regions, such as forexample, those of about 950, about 900, about 850, about 800, about 750,about 700, about 650, about 600, about 550, about 500, about 450, about400, about 350, about 300, about 250, about 200, about 150, or evenabout 100 amino acids or so in length.

[0038] In similar fashion, the polypeptides and peptides of the presentinvention may comprise even smaller contiguous amino acid codingregions, such as for example, those of about 95, about 90, about 85,about 80, about 75, about 70, about 65, about 60, about 55, about 50,about 45, about 40, about 35, about 30, about 25, about 20, about 15, oreven about 9 amino acids or so in length.

[0039] In all such embodiments, those peptides and polypeptides havingintermediate lengths including all integers within the preferred ranges(e.g., those peptides and polypeptides that comprise at least a firstcoding region of at least about 94, about 93, about 92, about 91, about89, about 88, about 87, about 86, about 84, about 83, about 82, about81, about 79, about 78, about 77, about 76, about 74, about 73, about72, about 71, about 69, about 68, about 67, about 66 or so amino acidsin length, etc.) are all contemplated to fall within the scope of thepresent invention.

[0040] In particular embodiments, the peptides and polypeptides of thepresent invention may comprise a sequence of at least about 9, or about10, or about 11, or about 12, or about 13, or about 14, or about 15, orabout 16, or about 17, or about 18, or about 19, or about 20, or about21, or about 22, or about 23, or about 24, or about 25, or about 26, orabout 27, or about 28, or about 29, or about 30, or about 31, or about32, or about 33, or about 34, or about 35, or about 36, or about 37, orabout 38, or about 39, or about 40, or about 41, or about 42, or about43, or about 44, or about 45, or about 46, or about 47, or about 48, orabout 49, or about 50 contiguous amino acids as disclosed in any one ormore of SEQ ID NO:9611 through SEQ ID NO:10466 herein.

[0041] In other embodiments, the peptides and polypeptides of thepresent invention may comprise a sequence of at least about 51, or about52, or about 53, or about 54, or about 55, or about 56, or about 57, orabout 58, or about 59, or about 60, or about 61, or about 62, or about63, or about 64, or about 65, or about 66, or about 67, or about 68, orabout 69, or about 70, or about 71, or about 72, or about 73, or about74, or about 75, or about 76, or about 77, or about 78, or about 79, orabout 80, or about 81, or about 82, or about 83, or about 84, or about85, or about 86, or about 87, or about 88, or about 89, or about 90,about 91, or about 92, or about 93, or about 94, or about 95, or about96, or about 97, or about 98, or about 99, or 100 contiguous amino acidsas disclosed in any one or more of SEQ ID NO:9611 through SEQ IDNO:10466 herein.

[0042] In still other embodiments, the preferred peptides andpolypeptides of the present invention comprise a sequence of at leastabout 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, or 400or more contiguous amino acids as disclosed in any one or more of SEQ IDNO:9611 through SEQ ID NO:10466 herein.

[0043] The polypeptides of the invention typically will comprise atleast a first contiguous amino acid sequence according to any one of SEQID NO:9611 through SEQ ID NO:10466, but may also, optionally comprise atleast a second, at least a third, or even at least a fourth or greatercontiguous amino acid sequence according to any one of SEQ ID NO:9611through SEQ ID NO:10466. A single polypeptide may contain only a singlecoding region, or alternatively, a single polypeptide may comprise aplurality of identical or distinctly different contiguous amino acidsequences in accordance with any one of SEQ ID NO:9611 through SEQ IDNO:10466. In fact, the polypeptide may comprise a plurality of the samecontiguous amino acid sequences, or they may comprise one or moredifferent contiguous amino acid sequences disclosed in SEQ ID NO:9611through SEQ ID NO:10466. For example, a single polypeptide can comprisea single contiguous amino acid sequence from one or more of SEQ IDNO:9611 through SEQ ID NO:10466, or alternatively, may comprise two ormore distinctly different contiguous amino acid sequences from one ormore of SEQ ID NO:9611 through SEQ ID NO:10466. In fact, the polypeptidemay comprise 2, 3, 4, or even 5 distinct contiguous amino sequences asdisclosed in any of SEQ ID NO:9611 through SEQ ID NO:10466.Alternatively, a single polypeptide may comprise 2, 3, 4, or even 5distinct coding regions. For example, a polypeptide may comprise atleast a first coding region that comprises a first contiguous amino acidsequence as disclosed in any of SEQ ID NO:9611 through SEQ ID NO:10466,and at least a second coding region that comprises a second contiguousamino acid sequence as disclosed in any of SEQ ID NO:9611 through SEQ IDNO:10466. In contrast, a polypeptide may comprise at least a firstcoding region that comprises a first contiguous amino acid sequence asdisclosed in any of SEQ ID NO:9611 through SEQ ID NO:10466, and at leasta second coding region that comprises a second distinctly differentpeptide or polypeptide, such as for example, an adjuvant or animmunostimulant peptide or polypeptide.

[0044] In such cases, the two coding regions may be separate on the samepolypeptide, or the two coding regions may be operatively attached, eachin the correct reading frame, such that a fusion polypeptide isproduced, in which the first amino acid sequence of the first codingregion is linked to the second amino acid sequence of the second codingregion.

[0045] Throughout this disclosure, a phrase such as “a sequence asdisclosed in SEQ ID NO:9598 to SEQ ID NO:9601” is intended to encompassany and all contiguous sequences disclosed by any one of these sequenceidentifiers. That is to say, “a sequence as disclosed in any of SEQ IDNO:9598 through SEQ ID NO:9601” means any sequence that is disclosed inany one of SEQ ID NO:9598, SEQ ID NO:9599, SEQ ID NO:9600, or SEQ IDNO:9601. Likewise, “a sequence as disclosed in any of SEQ ID NOs:9622 to9634” means any sequence that is disclosed in any one of SEQ ID NO:9622,SEQ ID NO:9623, SEQ ID NO:9624, SEQ ID NO:9625, SEQ ID NO:9626, SEQ IDNO:9627, SEQ ID NO:9628, SEQ ID NO:9629, SEQ ID NO:9630, SEQ ID NO:9631,SEQ ID NO:9632, SEQ ID NO:9633, or SEQ ID NO:9634, and so forth.

[0046] Likewise, “at least a first sequence from any one of SEQ IDNO:9652 to SEQ ID NO:9659” is intended to refer to a first sequence thatis disclosed in any one of SEQ ID NO:9652, SEQ ID NO:9653, SEQ IDNO:9654, SEQ ID NO:9655, SEQ ID NO:9656, SEQ ID NO:9657, SEQ ID NO:9658,or SEQ ID NO:9659.

[0047] It will also be understood that the kits, and compositions of thepresent invention comprise in an overall and general sense at least oneor more particular polynucleotides, polypeptides, and peptides thatcomprise one or more contiguous sequence regions from one or more of thenucleic acid sequences disclosed herein in SEQ ID NO:9598 through SEQ IDNO:9610 or from one or more of the amino acid sequences disclosed hereinin SEQ ID NO:9611 through SEQ ID NO:10466, and that such peptide,polypeptide and polynucleotide compositions may be used in one or moreof the particular methods and uses disclosed herein for the diagnosis,detection, prophylaxis, and therapy of one or more hematologicalcancers, and in particular, lymphomas of a variety of specific types. Itwill also be understood to the skilled artisan having benefit of theteachings of the present Specification, that the peptide and polypeptidecompositions may be used to generate a T cell or an immune response inan animal, and that such compositions may also be administered to ananimal from which immunospecific antibodies and antigen bindingfragments may be isolated or identified that specifically bind to suchpeptides or polypeptides. Such an artisan will also recognize that thepolynucleotides identified by the present disclosure may be used toproduce such peptides, polypeptides, antibodies, and antigen bindingfragments, by recombinant protein production methodologies that are alsowithin the capability of the skilled artisan having benefit of thespecific amino acid and nucleic acid sequences provided herein.

[0048] Likewise, it will be understood by a skilled artisan in thefield, that one or more of the disclosed compositions may used in one ormore diagnostic or detection methodologies to identify certainantibodies, peptides, polynucleotides, or polypeptides in a biologicalsample, in a host cell, or even within the body or tissues of an animal.It will be understood by a skilled artisan in the field, that one ormore of the disclosed nucleic acid or amino acid compositions may usedin the preparation or manufacture of one or more medicaments for use inthe diagnosis, detection, prognosis, prophylaxis, or therapy of one ormore hematological malignancies in an animal, and particularly thosemalignant conditions disclosed and claimed herein.

[0049] It will also be readily apparent to those of skill in the art,that the methods, kits, and uses, of the present invention preferablyemploy one or more of the compounds and/or compositions disclosed hereinthat comprise one or more contiguous nucleotide sequences as may bepresented in SEQ ID NO:9598 through SEQ ID NO:9610 of the attachedsequence listing.

[0050] Likewise, it will also be readily apparent to those of skill inthe art, that the methods, kits, and uses, of the present invention mayalso employ one or more of the compounds and compositions disclosedherein that comprise one or more contiguous amino acid sequences as maybe presented in SEQ ID NO:9611 through SEQ ID NO:10466 of the attachedsequence listing.

3. BRIEF DESCRIPTION OF THE DRAWINGS AND THE APPENDICES

[0051] The invention may be understood by reference to the followingdescription taken in conjunction with the accompanying drawings, inwhich like reference numerals identify like elements, and in which:

[0052]FIG. 1 illustrates a schematic outline of the microarray chiptechnology approach used to identify the cDNA targets of the presentinvention as described Section 5.1;

[0053]FIG. 2 illustrates a schematic outline of the general protocol forin vitro whole gene CD8⁺ T cell priming procedure used to generateantigen-specific lines and to identify clones of interest;

[0054]FIG. 3 illustrates a schematic outline of the general protocol forin vitro whole gene CD4⁺ T cell priming procedure used to generateantigen-specific lines and to identify clones of interest;

[0055]FIG. 4 illustrates the results of Coronin 1A mRNA expression inlymphoma patients and normal tissues as determined by real-time PCR.

[0056]FIG. 5 illustrates the results of TCL extended normal panel.

[0057]FIG. 6 is a diagram of the genomic locus encoding LY1448 proteinindicating the positions of exons and introns. Also diagramed are theexons contained in the LY1448 protein, the alternatively splicedfragment LS 1384258.1 and LY1448P, and the exons in SPAP1.

[0058]FIG. 7 illustrates the results of analyzing SEQ ID NO:9611 withthe program TSITES.

[0059]FIG. 8 illustrates the results of a western blot containing wholecell lysates of HEK293 cells transiently transfected with controlvectors and a recombinant vector encoding a LY1448-FLAG fusion proteinand probed with an anti-FLAG mAb.

[0060]FIG. 9 illustrates the results of cell surface labelingexperiment. HEK293 cells, transiently transfected with the recombinantvector LY1448P-FLAG/pCEP4, were biotinylated on the cell surface. Thecells were washed and lysed and the FLAG fusion proteins wereimmunoprecipitated with anti-FLAG Sepharose, were separated onpolyacrylamide gels, were electrobloted and reacted with avidin-HRP andECL reagent.

4. DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0061] In order that the invention herein described may be more fullyunderstood, the following description of various illustrativeembodiments is set forth.

[0062] The present invention is generally directed to compositions andmethods for the immunotherapy and diagnosis of Hematologicalmalignancies, such as B cell leukemias and lymphomas and multiplemyelomas.

[0063] 4.1 Methods of Nucleic Acid Delivery and DNA Transfection

[0064] In certain embodiments, it is contemplated that one or more RNAor DNA and/or substituted polynucleotide compositions disclosed hereinwill be used to transfect an appropriate host cell. Technology forintroduction of RNAs and DNAs, and vectors comprising them into suitablehost cells is well known to those of skill in the art. In particular,such polynucleotides may be used to genetically transform one or morehost cells, when therapeutic administration of one or more activepeptides, compounds or vaccines is achieved through the expression ofone or more polynucleotide constructs that encode one or moretherapeutic compounds of interest.

[0065] A variety of means for introducing polynucleotides and/orpolypeptides into suitable target cells is known to those of skill inthe art. For example, when polynucleotides are contemplated for deliveryto cells, several non-viral methods for the transfer of expressionconstructs into cultured mammalian cells are available to the skilledartisan for his use. These include, for example, calcium phosphateprecipitation (Graham and Van Der Eb, 1973; Chen and Okayama, 1987;Rippe et al., 1990); DEAE-dextran precipitation (Gopal, 1985);electroporation (Wong and Neumann, 1982; Fromm et al., 1985; Tur-Kaspaet al., 1986; Potter et al., 1984; Suzuki et al., 1998; Vanbever et al.,1998), direct microinjection (Capecchi, 1980; Harland and Weintraub,1985), DNA-loaded liposomes (Nicolau and Sene, 1982; Fraley et al.,1979; Takakura, 1998) and lipofectamine-DNA complexes, cell sonication(Fechheimer et al., 1987), gene bombardment using high velocitymicroprojectiles (Yang et al., 1990; Klein et al., 1992), andreceptor-mediated transfection (Curiel et al., 1991; Wagner et al.,1992; Wu and Wu, 1987; Wu and Wu, 1988). Some of these techniques may besuccessfully adapted for in vivo or ex vivo use.

[0066] A bacterial cell, a yeast cell, or an animal cell transformedwith one or more of the disclosed expression vectors represent animportant aspect of the present invention. Such transformed host cellsare often desirable for use in the expression of the various DNA geneconstructs disclosed herein. In some aspects of the invention, it isoften desirable to modulate, regulate, or otherwise control theexpression of the gene segments disclosed herein. Such methods areroutine to those of skill in the molecular genetic arts. Typically, whenincreased or over-expression of a particular gene is desired, variousmanipulations may be employed for enhancing the expression of themessenger RNA, particularly by using an active promoter, and inparticular, a tissue-specific promoter such as those disclosed herein,as well as by employing sequences, which enhance the stability of themessenger RNA in the particular transformed host cell.

[0067] Typically, the initiation and translational termination regionwill involve stop codon(s), a terminator region, and optionally, apolyadenylation signal. In the direction of transcription, namely in the5′ to 3′ direction of the coding or sense sequence, the construct willinvolve the transcriptional regulatory region, if any, and the promoter,where the regulatory region may be either 5′ or 3′ of the promoter, theribosomal binding site, the initiation codon, the structural gene havingan open reading frame in phase with the initiation codon, the stopcodon(s), the polyadenylation signal sequence, if any, and theterminator region. This sequence as a double strand may be used byitself for transformation of a microorganism or eukaryotic host, butwill usually be included with a DNA sequence involving a marker, wherethe second DNA sequence may be joined to the expression construct duringintroduction of the DNA into the host.

[0068] Where no functional replication system is present, the constructwill also preferably include a sequence of at least about 30 or about 40or about 50 base pairs (bp) or so, preferably at least about 60, about70, about 80, or about 90 to about 100 or so bp, and usually not morethan about 500 to about 1000 or so bp of a sequence homologous with asequence in the host. In this way, the probability of legitimaterecombination is enhanced, so that the gene will be integrated into thehost and stably maintained by the host. Desirably, the regulatoryregions of the expression construct will be in close proximity to (andalso operably positioned relative to) the selected therapeutic geneproviding for complementation as well as the gene providing for thecompetitive advantage. Therefore, in the event that the therapeutic geneis lost, the resulting organism will be likely to also lose the geneproviding for the competitive advantage, so that it will be unable tocompete in the environment with the gene retaining the intact construct.

[0069] The selected therapeutic gene can be introduced between thetranscriptional and translational initiation region and thetranscriptional and translational termination region, so as to be underthe regulatory control of the initiation region. This construct may beincluded in a plasmid, which will include at least one replicationsystem, but may include more than one, where one replication system isemployed for cloning during the development of the plasmid and thesecond replication system is necessary for functioning in the ultimatehost, in this case, a mammalian host cell. In addition, one or moremarkers may be present, which have been described previously. Whereintegration is desired, the plasmid will desirably include a sequencehomologous with the host genome.

[0070] Genes or other nucleic acid segments, as disclosed herein, can beinserted into host cells using a variety of techniques that are wellknown in the art. Five general methods for delivering a nucleic segmentinto cells have been described: (1) chemical methods (Graham and Van DerEb, 1973); (2) physical methods such as microinjection (Capecchi, 1980),electroporation (U.S. Pat. No. 5,472,869; Wong and Neumann, 1982; Frommet al., 1985), microprojectiles bombardment (U.S. Pat. No. 5,874,265,specifically incorporated herein by reference in its entirety), “genegun” (Yang et al., 1990); (3) viral vectors (Eglitis and Anderson,1988); (4) receptor-mediated mechanisms (Curiel et al., 1991; Wagner etal., 1992); and (5) bacterial-mediated transformation.

[0071] 4.2 Hematological Malignancy Related-Specific Antibodies andAntigen-Binding Fragments Thereof

[0072] The present invention further provides antibodies andantigen-binding fragments thereof, that specifically bind to (or areimmunospecific for) at least a first peptide or peptide variant asdisclosed herein. As used herein, an antibody or an antigen-bindingfragment is said to “specifically bind” to a peptide if it reacts at adetectable level (within, for example, an ELISA) with the peptide, anddoes not react detectably with unrelated peptides or proteins undersimilar conditions. As used herein, “binding” refers to a non-covalentassociation between two separate molecules such that a “complex” isformed. The ability to bind may be evaluated by, for example,determining a binding constant for the formation of the complex. Thebinding constant is the value obtained when the concentration of thecomplex is divided by the product of the component concentrations. Inthe context of the present invention, in general, two compounds are saidto “bind” when the binding constant for complex formation exceeds about10³ L/mol. The binding constant maybe determined using methods wellknown in the art.

[0073] Any agent that satisfies the above requirements may be a bindingagent. In illustrative embodiments, a binding agent is an antibody or anantigen-binding fragment thereof. Such antibodies may be prepared by anyof a variety of techniques known to those of ordinary skill in the art(Harlow and Lane, 1988). In general, antibodies can be produced by cellculture techniques, including the generation of monoclonal antibodies asdescribed herein, or via transfection of antibody genes into suitablebacterial or mammalian cell hosts, in order to allow for the productionof recombinant antibodies. In one technique, an immunogen comprising thepeptide is initially injected into any of a wide variety of mammals(e.g., mice, rats, rabbits, sheep or goats). In this step, the peptidesof this invention may serve as the immunogen without modification.Alternatively, particularly for relatively short peptides, a superiorimmune response may be elicited if the peptide is joined to a carrierprotein, such as bovine serum albumin or keyhole limpet hemocyanin. Theimmunogen is injected into the animal host, preferably according to apredetermined schedule incorporating one or more booster immunizations,and the animals are bled periodically. Polyclonal antibodies specificfor the peptide may then be purified from such antisera by, for example,affinity chromatography using the peptide coupled to a suitable solidsupport.

[0074] Monoclonal antibodies specific for the antigenic peptide ofinterest may be prepared, for example, using the technique of Kohler andMilstein (1976) and improvements thereto. Briefly, these methods involvethe preparation of immortal cell lines capable of producing antibodieshaving the desired specificity (i.e., reactivity with the peptide ofinterest). Such cell lines may be produced, for example, from spleencells obtained from an animal immunized as described above. The spleencells are then immortalized by, for example, fusion with a myeloma cellfusion partner, preferably one that is syngeneic with the immunizedanimal. A variety of fusion techniques may be employed. For example, thespleen cells and myeloma cells may be combined with a nonionic detergentfor a few minutes and then plated at low density on a selective mediumthat supports the growth of hybrid cells, but not myeloma cells. Apreferred selection technique uses HAT (hypoxanthine, aminopterin,thymidine) selection. After a sufficient time, usually about 1 to 2weeks, colonies of hybrids are observed. Single colonies are selectedand their culture supernatants tested for binding activity against thepeptide. Hybridomas having high reactivity and specificity arepreferred.

[0075] Monoclonal antibodies may be isolated from the supernatants ofgrowing hybridoma colonies. In addition, various techniques may beemployed to enhance the yield, such as injection of the hybridoma cellline into the peritoneal cavity of a suitable vertebrate host, such as amouse. Monoclonal antibodies may then be harvested from the ascitesfluid or the blood. Contaminants may be removed from the antibodies byconventional techniques, such as chromatography, gel filtration,precipitation, and extraction. The peptides of this invention may beused in the purification process in, for example, an affinitychromatography step.

[0076] Within certain embodiments, the use of antigen-binding fragmentsof antibodies may be preferred. Such fragments include Fab fragments,which may be prepared using standard techniques. Briefly,immunoglobulins may be purified from rabbit serum by affinitychromatography on Protein A bead columns (Harlow and Lane, 1988) anddigested by papain to yield Fab and Fc fragments. The Fab and Fcfragments may be separated by affinity chromatography on Protein A beadcolumns.

[0077] Monoclonal antibodies and fragments thereof may be coupled to oneor more therapeutic agents. Suitable agents in this regard includeradioactive tracers and chemotherapeutic agents, which may be used, forexample, to purge autologous bone marrow in vitro). Representativetherapeutic agents include radionuclides, differentiation inducers,drugs, toxins, and derivatives thereof. Preferred radionuclides include⁹⁰Y, ¹²³I, ¹²⁵I, ¹³¹I, ¹⁸⁶Re, ¹⁸⁸Re, ²¹¹At, and ²¹²Bi. Preferred drugsinclude methotrexate, and pyrimidine and purine analogs. Preferreddifferentiation inducers include phorbol esters and butyric acid.Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin,gelonin, Pseudomonas exotoxin, Shigella toxin, and pokeweed antiviralprotein. For diagnostic purposes, coupling of radioactive agents may beused to facilitate tracing of metastases or to determine the location ofhematological malignancy related-positive tumors.

[0078] A therapeutic agent may be coupled (e.g., covalently bonded) to asuitable monoclonal antibody either directly or indirectly (e.g., via alinker group). A direct reaction between an agent and an antibody ispossible when each possesses a substituent capable of reacting with theother. For example, a nucleophilic group, such as an amino or sulfhydrylgroup, on one may be capable of reacting with a carbonyl-containinggroup, such as an anhydride or an acid halide, or with an alkyl groupcontaining a good leaving group (e.g., a halide) on the other.

[0079] Alternatively, it may be desirable to couple a therapeutic agentand an antibody via a linker group. A linker group can function as aspacer to distance an antibody from an agent in order to avoidinterference with binding capabilities. A linker group can also serve toincrease the chemical reactivity of a substituent on an agent or anantibody, and thus increase the coupling efficiency. An increase inchemical reactivity may also facilitate the use of agents, or functionalgroups on agents, which otherwise would not be possible.

[0080] It will be evident to those skilled in the art that a variety ofbifunctional or polyfunctional reagents, both homo- andhetero-functional (such as those described in the catalog of the PierceChemical Co., Rockford, Ill.), may be employed as the linker group.Coupling may be affected, for example, through amino groups, carboxylgroups, and sulfhydryl groups or oxidized carbohydrate residues. Thereare numerous references describing such methodology, e.g., U.S. Pat. No.4,671,958.

[0081] Where a therapeutic agent is more potent when free from theantibody portion of the immunoconjugates of the present invention, itmay be desirable to use a linker group that is cleavable during or uponinternalization into a cell. A number of different cleavable linkergroups have been described. The mechanisms for the intracellular releaseof an agent from these linker groups include cleavage by reduction of adisulfide bond (U.S. Pat. No. 4,489,710), by irradiation of aphotolabile bond (U.S. Pat. No. 4,625,014), by hydrolysis of derivatizedamino acid side chains (U.S. Pat. No. 4,638,045), by serumcomplement-mediated hydrolysis (U.S. Pat. No. 4,671,958), andacid-catalyzed hydrolysis (U.S. Pat. No. 4,569,789).

[0082] It may be desirable to couple more than one agent to an antibody.In one embodiment, multiple molecules of an agent are coupled to oneantibody molecule. In another embodiment, more than one type of agentmay be coupled to one antibody. Regardless of the particular embodiment,immunoconjugates with more than one agent may be prepared in a varietyof ways. For example, more than one agent may be coupled directly to anantibody molecule, or linkers that provide multiple sites for attachmentcan be used. Alternatively, a carrier can be used. A carrier may bearthe agents in a variety of ways, including covalent bonding eitherdirectly or via a linker group. Suitable carriers include proteins suchas albumins (U.S. Pat. No. 4,507,234), peptides and polysaccharides suchas aminodextran (U.S. Pat. No. 4,699,784). A carrier may also bear anagent by noncovalent bonding or by encapsulation, such as within aliposome vesicle (U.S. Pat. No. 4,429,008 and U.S. Pat. No. 4,873,088).Carriers specific for radionuclide agents include radiohalogenated smallmolecules and chelating compounds. For example, U.S. Pat. No. 4,735,792discloses representative radiohalogenated small molecules and theirsynthesis. A radionuclide chelate may be formed from chelating compoundsthat include those containing nitrogen and sulfur atoms as the donoratoms for binding the metal, or metal oxide, radionuclide. For example,U.S. Pat. No. 4,673,562 discloses representative chelating compounds andtheir synthesis.

[0083] A variety of routes of administration for the antibodies andimmunoconjugates may be used. Typically, administration will beintravenous, intramuscular, subcutaneous or in the bed of a resectedtumor. It will be evident that the precise dose of theantibody/immunoconjugate will vary depending upon the antibody used, theantigen density on the tumor, and the rate of clearance of the antibody.

[0084] Also provided herein are anti-idiotypic antibodies that mimic animmunogenic portion of hematological malignancy related. Such antibodiesmay be raised against an antibody, or an antigen-binding fragmentthereof, that specifically binds to an immunogenic portion ofhematological malignancy related, using well-known techniques.Anti-idiotypic antibodies that mimic an immunogenic portion ofhematological malignancy related are those antibodies that bind to anantibody, or antigen-binding fragment thereof, that specifically bindsto an immunogenic portion of hematological malignancy related, asdescribed herein.

[0085] Irrespective of the source of the original hematologicalmalignancy related peptide-specific antibody, the intact antibody,antibody multimers, or any one of a variety of functional,antigen-binding regions of the antibody may be used in the presentinvention. Exemplary functional regions include scFv, Fv, Fab′, Fab andF(ab′)₂ fragments of the hematological malignancy relatedpeptide-specific antibodies. Techniques for preparing such constructsare well known to those in the art and are further exemplified herein.

[0086] The choice of antibody construct may be influenced by variousfactors. For example, prolonged half-life can result from the activereadsorption of intact antibodies within the kidney, a property of theFc piece of immunoglobulin. IgG based antibodies, therefore, areexpected to exhibit slower blood clearance than their Fab′ counterparts.However, Fab′ fragment-based compositions will generally exhibit bettertissue penetrating capability.

[0087] Antibody fragments can be obtained by proteolysis of the wholeimmunoglobulin by the non-specific thiol protease, papain. Papaindigestion yields two identical antigen-binding fragments, termed “Fabfragments,” each with a single antigen-binding site, and a residual “Fcfragment.”

[0088] Papain should first be activated by reducing the sulfhydryl groupin the active site with cysteine, 2-mercaptoethanol or dithiothreitol.Heavy metals in the stock enzyme should be removed by chelation withEDTA (2 mM) to ensure maximum enzyme activity. Enzyme and substrate arenormally mixed together in the ratio of 1:100 by weight. Afterincubation, the reaction can be stopped by irreversible alkylation ofthe thiol group with iodoacetamide or simply by dialysis. Thecompleteness of the digestion should be monitored by SDS-PAGE and thevarious fractions separated by Protein A-Sepharose or ion exchangechromatography.

[0089] The usual procedure for preparation of F(ab′)₂ fragments from IgGof rabbit and human origin is limited proteolysis by the enzyme pepsin.The conditions, 100× antibody excess wt./wt. in acetate buffer at pH4.5, 37° C., suggest that antibody is cleaved at the C-terminal side ofthe inter-heavy-chain disulfide bond. Rates of digestion of mouse IgGmay vary with subclass and it may be difficult to obtain high yields ofactive F(ab′)₂ fragments without some undigested or completely degradedIgG. In particular, IgG_(2b) is highly susceptible to completedegradation. The other subclasses require different incubationconditions to produce optimal results, all of which is known in the art.

[0090] Pepsin treatment of intact antibodies yields an F(ab′)₂ fragmentthat has two antigen-combining sites and is still capable ofcross-linking antigen. Digestion of rat IgG by pepsin requiresconditions including dialysis in 0.1 M acetate buffer, pH 4.5, and thenincubation for four hrs with 1% wt./wt. pepsin; IgG₁ and IgG_(2a)digestion is improved if first dialyzed against 0.1 M formate buffer, pH2.8, at 4° C., for 16 hrs followed by acetate buffer. IgG_(2b) givesmore consistent results with incubation in staphylococcal V8 protease(3% wt./wt.) in 0.1 M sodium phosphate buffer, pH 7.8, for four hrs at37° C.

[0091] A Fab fragment also contains the constant domain of the lightchain and the first constant domain (CH1) of the heavy chain. Fab′fragments differ from Fab fragments by the addition of a few residues atthe carboxyl terminus of the heavy chain CH1 domain including one ormore cysteine(s) from the antibody hinge region. F(ab′)₂ antibodyfragments were originally produced as pairs of Fab′ fragments that havehinge cysteines between them. Other chemical couplings of antibodyfragments are also known.

[0092] The term “variable,” as used herein in reference to antibodies,means that certain portions of the variable domains differ extensivelyin sequence among antibodies, and are used in the binding andspecificity of each particular antibody to its particular antigen.However, the variability is not evenly distributed throughout thevariable domains of antibodies. It is concentrated in three segmentstermed “hypervariable regions,” both in the light chain and the heavychain variable domains.

[0093] The more highly conserved portions of variable domains are calledthe framework region (FR). The variable domains of native heavy andlight chains each comprise four FRs (FR1, FR2, FR3 and FR4,respectively), largely adopting a β-sheet configuration, connected bythree hypervariable regions, which form loops connecting, and in somecases, forming part of, the β-sheet structure.

[0094] The hypervariable regions in each chain are held together inclose proximity by the FRs and, with the hypervariable regions from theother chain, contribute to the formation of the antigen-binding site ofantibodies (Kabat et al., 1991, specifically incorporated herein byreference). The constant domains are not involved directly in binding anantibody to an antigen, but exhibit various effector functions, such asparticipation of the antibody in antibody-dependent cellular toxicity.

[0095] The term “hypervariable region,” as used herein, refers to theamino acid residues of an antibody that are responsible forantigen-binding. The hypervariable region comprises amino acid residuesfrom a “complementarity determining region” or “CDR” (i.e. residues24-34 (L1), 50-56 (L2) and 89-97 (L3) in the light chain variable domainand 31-35 (H1), 50-56 (H2) and 95-102 (H3) in the heavy chain variabledomain (Kabat et al., 1991, specifically incorporated herein byreference) and/or those residues from a “hypervariable loop” (i.e.,residues 26-32 (L1), 50-52(L2) and 91-96 (L3) in the light chainvariable domain and 26-32 (H1), 53-55 (H2) and 96-101 (H3) in the heavychain variable domain). “Framework” or “FR” residues are those variabledomain residues other than the hypervariable region residues as hereindefined.

[0096] An “Fv” fragment is the minimum antibody fragment that contains acomplete antigen-recognition and binding site. This region consists of adimer of one heavy chain and one light chain variable domain in tight,con-covalent association. It is in this configuration that threehypervariable regions of each variable domain interact to define anantigen-binding site on the surface of the V_(H)-V_(L) dimer.Collectively, six hypervariable regions confer antigen-bindingspecificity to the antibody. However, even a single variable domain (orhalf of an Fv comprising only three hypervariable regions specific foran antigen) has the ability to recognize and bind antigen, although at alower affinity than the entire binding site.

[0097] “Single-chain Fv” or “sFv” antibody fragments comprise the V_(H)and V_(L) domains of antibody, wherein these domains are present in asingle polypeptide chain. Generally, the Fv polypeptide furthercomprises a polypeptide linker between the V_(H) and V_(L) domains thatenables the sFv to form the desired structure for antigen binding.

[0098] “Diabodies” are small antibody fragments with two antigen-bindingsites, which fragments comprise a heavy chain variable domain (V_(H))connected to a light chain variable domain (V_(L)) in the samepolypeptide chain (V_(H)-V_(L)). By using a linker that is too short toallow pairing between the two domains on the same chain, the domains areforced to pair with the complementary domains of another chain andcreate two antigen-binding sites. Diabodies are described in EuropeanPat. Appl. No. EP 404,097 and Intl. Pat. Appl. Publ. No. WO 93/11161,each specifically incorporated herein by reference. “Linear antibodies”,which can be bispecific or monospecific, comprise a pair of tandem Fdsegments (V_(H)-C_(H)1-V_(H)-C_(H)1) that form a pair of antigen bindingregions, as described in Zapata et al. (1995), specifically incorporatedherein by reference.

[0099] Other types of variants are antibodies with improved biologicalproperties relative to the parent antibody from which they aregenerated. Such variants, or second-generation compounds, are typicallysubstitutional variants involving one or more substituted hypervariableregion residues of a parent antibody. A convenient way for generatingsuch substitutional variants is affinity maturation using phage display.

[0100] In affinity maturation using phage display, several hypervariableregion sites (e.g., 6 to 7 sites) are mutated to generate all possibleamino substitutions at each site. The antibody variants thus generatedare displayed in a monovalent fashion from filamentous phage particlesas fusions to the gene III product of M13 packaged within each particle.The phage-displayed variants are then screened for their biologicalactivity (e.g., binding affinity) as herein disclosed. In order toidentify candidate hypervariable region sites for modification,alanine-scanning mutagenesis can be performed on hypervariable regionresidues identified as contributing significantly to antigen binding.

[0101] Alternatively, or in addition, the crystal structure of theantigen-antibody complex be delineated and analyzed to identify contactpoints between the antibody and target. Such contact residues andneighboring residues are candidates for substitution. Once such variantsare generated, the panel of variants is subjected to screening, andantibodies with analogues but different or even superior properties inone or more relevant assays are selected for further development.

[0102] In using a Fab′ or antigen binding fragment of an antibody, withthe attendant benefits on tissue penetration, one may derive additionaladvantages from modifying the fragment to increase its half-life. Avariety of techniques may be employed, such as manipulation ormodification of the antibody molecule itself, and also conjugation toinert carriers. Any conjugation for the sole purpose of increasinghalf-life, rather than to deliver an agent to a target, should beapproached carefully in that Fab′ and other fragments are chosen topenetrate tissues. Nonetheless, conjugation to non-protein polymers,such PEG and the like, is contemplated.

[0103] Modifications other than conjugation are therefore based uponmodifying the structure of the antibody fragment to render it morestable, and/or to reduce the rate of catabolism in the body. Onemechanism for such modifications is the use of D-amino acids in place ofL-amino acids. Those of ordinary skill in the art will understand thatthe introduction of such modifications needs to be followed by rigoroustesting of the resultant molecule to ensure that it still retains thedesired biological properties. Further stabilizing modifications includethe use of the addition of stabilizing moieties to either the N-terminalor the C-terminal, or both, which is generally used to prolong thehalf-life of biological molecules. By way of example only, one may wishto modify the termini by acylation or amination.

[0104] Moderate conjugation-type modifications for use with the presentinvention include incorporating a salvage receptor binding epitope intothe antibody fragment. Techniques for achieving this include mutation ofthe appropriate region of the antibody fragment or incorporating theepitope as a peptide tag that is attached to the antibody fragment.Intl. Pat. Appl. Publ. No. WO 96/32478 is specifically incorporatedherein by reference for the purposes of further exemplifying suchtechnology. Salvage receptor binding epitopes are typically regions ofthree or more amino acids from one or two lops of the Fc domain that aretransferred to the analogous position on the antibody fragment. Thesalvage receptor-binding epitopes disclosed in Intl. Pat. Appl. Publ.No. WO 98/45331 are incorporated herein by reference for use with thepresent invention.

[0105] 4.3 T Cell Compositions Specific for HematologicalMalignancy-Related Peptides

[0106] Immunotherapeutic compositions may also, or alternatively,comprise T cells specific for hematological malignancy related. Suchcells may generally be prepared in vitro or ex vivo, using standardprocedures. For example, T cells may be present within (or isolatedfrom) bone marrow, peripheral blood or a fraction of bone marrow orperipheral blood of a mammal, such as a patient, using a commerciallyavailable cell separation system, such as the Isolex™ System, availablefrom Nexell Therapeutics, Inc. (Irvine, Calif.; see also U.S. Pat. No.5,240,856; U.S. Pat. No. 5,215,926; Intl. Pat. Appl. Publ. No. WO89/06280; Intl. Pat. Appl. Publ. No. WO 91/16116 and Intl. Pat. Appl.Publ. No. WO 92/07243). Alternatively, T cells may be derived fromrelated or unrelated humans, non-human mammals, cell lines or cultures.

[0107] T cells may be stimulated with hematological malignancy relatedpeptide, polynucleotide encoding a hematological malignancy relatedpeptide and/or an antigen-presenting cell (APC) that expresses ahematological malignancy related peptide. Such stimulation is performedunder conditions and for a time sufficient to permit the generation of Tcells that are specific for the hematological malignancy relatedpeptide. Preferably, a hematological malignancy related peptide orpolynucleotide is present within a delivery vehicle, such as amicrosphere, to facilitate the generation of antigen-specific T cells.Briefly, T cells, which may be isolated from a patient or a related orunrelated donor by routine techniques (such as by Ficoll/Hypaque®density gradient centrifugation of peripheral blood lymphocytes), areincubated with hematological malignancy related peptide. For example, Tcells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C. with hematological malignancy related peptide (e.g., 5 to 25 μg/ml)or cells synthesizing a comparable amount of hematological malignancyrelated peptide. It may be desirable to incubate a separate aliquot of aT cell sample in the absence of hematological malignancy related peptideto serve as a control.

[0108] T cells are considered to be specific for a hematologicalmalignancy related peptide if the T cells kill target cells coated witha hematological malignancy related peptide or expressing a gene encodingsuch a peptide. T cell specificity may be evaluated using any of avariety of standard techniques. For example, within a chromium releaseassay or proliferation assay, a stimulation index of more than two foldincrease in lysis and/or proliferation, compared to negative controls,indicates T cell specificity. Such assays may be performed, for example,as described in Chen et al. (1994). Alternatively, detection of theproliferation of T cells may be accomplished by a variety of knowntechniques. For example, T cell proliferation can be detected bymeasuring an increased rate of DNA synthesis (e.g., by pulse-labelingcultures of T cells with tritiated thymidine and measuring the amount oftritiated thymidine incorporated into DNA). Other ways to detect T cellproliferation include measuring increases in interleukin-2 (IL-2)production, Ca²⁺ flux, or dye uptake, such as3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium. Alternatively,synthesis of lymphokines (such as interferon-gamma) can be measured orthe relative number of T cells that can respond to a hematologicalmalignancy related peptide may be quantified. Contact with ahematological malignancy related peptide (200 ng/ml-100 μg/ml,preferably 100 ng/ml-25 μg/ml) for 3-7 days should result in at least atwo-fold increase in proliferation of the T cells and/or contact asdescribed above for 2-3 hrs should result in activation of the T cells,as measured using standard cytokine assays in which a two-fold increasein the level of cytokine release (e.g., TNF or IFN-γ) is indicative of Tcell activation (Coligan et al., 1998). hematological malignancy relatedspecific T cells may be expanded using standard techniques. Withinpreferred embodiments, the T cells are derived from a patient or arelated or unrelated donor and are administered to the patient followingstimulation and expansion.

[0109] T cells that have been activated in response to a hematologicalmalignancy related peptide, polynucleotide or hematological malignancyrelated-expressing APC may be CD4⁺ and/or CD8⁺. Specific activation ofCD4⁺ or CD8⁺T cells may be detected in a variety of ways. Methods fordetecting specific T cell activation include detecting the proliferationof T cells, the production of cytokines (e.g., lymphokines), or thegeneration of cytolytic activity (i.e., generation of cytotoxic T cellsspecific for hematological malignancy related). For CD4⁺ T cells, apreferred method for detecting specific T cell activation is thedetection of the proliferation of T cells. For CD8⁺ T cells, a preferredmethod for detecting specific T cell activation is the detection of thegeneration of cytolytic activity.

[0110] For therapeutic purposes, CD4⁺ or CD8⁺ T cells that proliferatein response to the hematological malignancy related peptide,polynucleotide or APC can be expanded in number either in vitro or invivo. Proliferation of such T cells in vitro may be accomplished in avariety of ways. For example, the T cells can be re-exposed tohematological malignancy related peptide, with or without the additionof T cell growth factors, such as interleukin-2, and/or stimulator cellsthat synthesize a hematological malignancy related peptide. The additionof stimulator cells is preferred where generating CD8⁺ T cell responses.T cells can be grown to large numbers in vitro with retention ofspecificity in response to intermittent restimulation with hematologicalmalignancy related peptide. Briefly, for the primary in vitrostimulation (IVS), large numbers of lymphocytes (e.g., greater than4×10⁷) may be placed in flasks with media containing human serum.hematological malignancy related peptide (e.g., peptide at 10 μg/ml) maybe added directly, along with tetanus toxoid (e.g., 5 μg/ml). The flasksmay then be incubated (e.g., 37° C. for 7 days). For a second IVS, Tcells are then harvested and placed in new flasks with 2-3×10⁷irradiated peripheral blood mononuclear cells. hematological malignancyrelated peptide (e.g., 10 μg/ml) is added directly. The flasks areincubated at 37° C. for 7 days. On day 2 and day 4 after the second IVS,2-5 units of interleukin-2 (IL-2) may be added. For a third IVS, the Tcells may be placed in wells and stimulated with the individual's ownEBV transformed B cells coated with the peptide. IL-2 may be added ondays 2 and 4 of each cycle. As soon as the cells are shown to bespecific cytotoxic T cells, they may be expanded using a 10-daystimulation cycle with higher IL-2 (20 units) on days 2, 4 and 6.

[0111] Alternatively, one or more T cells that proliferate in thepresence of hematological malignancy related peptide can be expanded innumber by cloning. Methods for cloning cells are well known in the art,and include limiting dilution. Responder T cells may be purified fromthe peripheral blood of sensitized patients by density gradientcentrifugation and sheep red cell rosetting and established in cultureby stimulating with the nominal antigen in the presence of irradiatedautologous filler cells. In order to generate CD4⁺ T cell lines,hematological malignancy related peptide is used as the antigenicstimulus and autologous peripheral blood lymphocytes (PBL) orlymphoblastoid cell lines (LCL) immortalized by infection with EpsteinBarr virus are used as antigen-presenting cells. In order to generateCD8⁺ T cell lines, autologous antigen-presenting cells transfected withan expression vector that produces hematological malignancy relatedpeptide may be used as stimulator cells. Established T cell lines may becloned 2-4 days following antigen stimulation by plating stimulated Tcells at a frequency of 0.5 cells per well in 96-well flat-bottom plateswith 1×10⁶ irradiated PBL or LCL cells and recombinant interleukin-2(rIL2) (50 U/ml). Wells with established clonal growth may be identifiedat approximately 2-3 weeks after initial plating and restimulated withappropriate antigen in the presence of autologous antigen-presentingcells, then subsequently expanded by the addition of low doses of rIL2(10 U/ml) 2-3 days following antigen stimulation. T cell clones may bemaintained in 24-well plates by periodic restimulation with antigen andrIL2 approximately every two weeks. Cloned and/or expanded cells may beadministered back to the patient as described, for example, by Chang etal., (1996).

[0112] Within certain embodiments, allogeneic T-cells may be primed(i.e., sensitized to hematological malignancy related) in vivo and/or invitro. Such priming may be achieved by contacting T cells with ahematological malignancy related peptide, a polynucleotide encoding sucha peptide or a cell producing such a peptide under conditions and for atime sufficient to permit the priming of T cells. In general, T cellsare considered to be primed if, for example, contact with ahematological malignancy related peptide results in proliferation and/oractivation of the T cells, as measured by standard proliferation,chromium release and/or cytokine release assays as described herein. Astimulation index of more than two fold increase in proliferation orlysis, and more than three fold increase in the level of cytokine,compared to negative controls indicates T-cell specificity. Cells primedin vitro may be employed, for example, within bone marrowtransplantation or as donor lymphocyte infusion.

[0113] T cells specific for hematological malignancy related can killcells that express hematological malignancy related protein.Introduction of genes encoding T-cell receptor (TCR) chains forhematological malignancy related are used as a means to quantitativelyand qualitatively improve responses to hematological malignancy relatedbearing leukemia and cancer cells. Vaccines to increase the number of Tcells that can react to hematological malignancy related positive cellsare one method of targeting hematological malignancy related bearingcells. T cell therapy with T cells specific for hematological malignancyrelated is another method. An alternative method is to introduce the TCRchains specific for hematological malignancy related into T cells orother cells with lytic potential. In a suitable embodiment, the TCRalpha and beta chains are cloned out from a hematological malignancyrelated specific T cell line and used for adoptive T cell therapy, suchas described in WO 96/30516, incorporated herein by reference.

[0114] 4.4 Pharmaceutical Compositions and Vaccine Formulations

[0115] Within certain aspects, peptides, polynucleotides, antibodiesand/or T cells may be incorporated into pharmaceutical compositions orimmunogenic compositions (i.e., vaccines). Alternatively, apharmaceutical composition may comprise an antigen-presenting cell(e.g., a dendritic cell) transfected with a hematological malignancyrelated polynucleotide such that the antigen-presenting cell expresses ahematological malignancy related peptide. Pharmaceutical compositionscomprise one or more such compounds or cells and a physiologicallyacceptable carrier or excipient. Vaccines may comprise one or more suchcompounds or cells and an immunostimulant, such as an adjuvant or aliposome (into which the compound is incorporated). An immunostimulantmay be any substance that enhances or potentiates an immune response(antibody- and/or cell-mediated) to an exogenous antigen. Examples ofimmunostimulants include adjuvants, biodegradable microspheres (e.g.,polylactic galactide) and liposomes (into which the compound isincorporated) (U.S. Pat. No. 4,235,877). Vaccine preparation isgenerally described in, for example, Powell and Newman (1995).Pharmaceutical compositions and vaccines within the scope of the presentinvention may also contain other compounds, which may be biologicallyactive or inactive. For example, one or more immunogenic portions ofother tumor antigens may be present, either incorporated into a fusionpeptide or as a separate compound, within the composition or vaccine.

[0116] Within certain embodiments, pharmaceutical compositions andvaccines are designed to elicit T cell responses specific for ahematological malignancy related peptide in a patient, such as a human.In general, T cell responses may be favored through the use ofrelatively short peptides (e.g., comprising less than 23 consecutiveamino acid residues of a native hematological malignancy relatedpeptide, preferably 4-16 consecutive residues, more preferably 8-16consecutive residues and still more preferably 8-10 consecutiveresidues). Alternatively, or in addition, a vaccine may comprise animmunostimulant that preferentially enhances a T cell response. In otherwords, the immunostimulant may enhance the level of a T cell response toa hematological malignancy related peptide by an amount that isproportionally greater than the amount by which an antibody response isenhanced. For example, when compared to a standard oil based adjuvant,such as CFA, an immunostimulant that preferentially enhances a T cellresponse may enhance a proliferative T cell response by at least twofold, a lytic response by at least 10%, and/or T cell activation by atleast two fold compared to hematological malignancy related-negativecontrol cell lines, while not detectably enhancing an antibody response.The amount by which a T cell or antibody response to a hematologicalmalignancy related peptide is enhanced may generally be determined usingany representative technique known in the art, such as the techniquesprovided herein.

[0117] A pharmaceutical composition or vaccine may contain DNA encodingone or more of the peptides as described above, such that the peptide isgenerated in situ. As noted above, the DNA may be present within any ofa variety of delivery systems known to those of ordinary skill in theart, including nucleic acid expression systems, bacterial and viralexpression systems and mammalian expression systems. Numerous genedelivery techniques are well known in the art (Rolland, 1998, andreferences cited therein). Appropriate nucleic acid expression systemscontain the necessary DNA, cDNA or RNA sequences for expression in thepatient (such as a suitable promoter and terminating signal). Bacterialdelivery systems involve the administration of a bacterium (such asBacillus-Calmette-Guerrin) that expresses an immunogenic portion of thepeptide on its cell surface or secretes such an epitope. In a preferredembodiment, the DNA may be introduced using a viral expression system(e.g., vaccinia or other pox virus, retrovirus, or adenovirus), whichmay involve the use of a non-pathogenic (defective), replicationcompetent virus (Fisher-Hoch et al., 1989; Flexner et al., 1989; Flexneret al., 1990; U.S. Pat. No. 4,603,112, U.S. Pat. No. 4,769,330, U.S.Pat. No. 5,017,487; Intl. Pat. Appl. Publ. No. WO 89/01973; U.S. Pat.No. 4,777,127; Great Britain Patent No. GB 2,200,651; European PatentNo. EP 0,345,242; Intl. Pat. Appl. Publ. No. WO 91/02805; Berkner, 1988;Rosenfeld et al., 1991; Kolls et al., 1994; Kass-Eisler et al., 1993;Guzman et al., 1993a; and Guzman et al., 1993). Techniques forincorporating DNA into such expression systems are well known to thoseof ordinary skill in the art. The DNA may also be “naked,” as described,for example, in Ulmer et al. (1993) and reviewed by Cohen (1993). Theuptake of naked DNA may be increased by coating the DNA ontobiodegradable beads, which are efficiently transported into the cells.It will be apparent that a vaccine may comprise both a polynucleotideand a peptide component. Such vaccines may provide for an enhancedimmune response.

[0118] As noted above, a pharmaceutical composition or vaccine maycomprise an antigen-presenting cell that expresses a hematologicalmalignancy related peptide. For therapeutic purposes, as describedherein, the antigen-presenting cell is preferably an autologousdendritic cell. Such cells may be prepared and transfected usingstandard techniques (Reeves et al., 1996; Tuting et al., 1998; and Nairet al., 1998). Expression of a hematological malignancy related peptideon the surface of an antigen-presenting cell may be confirmed by invitro stimulation and standard proliferation as well as chromium releaseassays, as described herein.

[0119] It will be apparent to those of ordinary skill in the art havingthe benefit of the present teachings that a vaccine may containpharmaceutically acceptable salts of the polynucleotides and peptidesprovided herein. Such salts may be prepared from pharmaceuticallyacceptable non-toxic bases, including organic bases (e.g., salts ofprimary, secondary and tertiary amines and basic amino acids) andinorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium andmagnesium salts). The phrases “pharmaceutically or pharmacologicallyacceptable” refer to molecular entities and compositions that do notproduce an adverse, allergic or other significant untoward reaction whenadministered to an animal, or a human, as appropriate. As used herein,“pharmaceutically acceptable carrier” includes any and all solvents,dispersion media, coatings, antibacterial and antifungal agents,isotonic and absorption delaying agents and the like. The use of suchmedia and agents for pharmaceutical active substances is well known inthe art. Except insofar as any conventional media or agent isincompatible with the active ingredient, its use in the therapeuticcompositions is contemplated. For human administration, preparationsshould meet sterility, pyrogenicity, and general safety and puritystandards as required by the Food and Drug Administration Office ofBiologics standards. Supplementary active ingredients can also beincorporated into the compositions.

[0120] While any suitable carrier known to those of ordinary skill inthe art may be employed in the pharmaceutical compositions of thisinvention, the type of carrier will vary depending on the mode ofadministration. Compositions of the present invention may be formulatedfor any appropriate manner of administration, including for example,topical, oral, nasal, intravenous, intracranial, intraperitoneal,subcutaneous or intramuscular administration. For parenteraladministration, such as subcutaneous injection, the carrier preferablycomprises water, saline, alcohol, a fat, a wax or a buffer. For oraladministration, any of the above carriers or a solid carrier, such asmannitol, lactose, starch, magnesium stearate, sodium saccharine,talcum, cellulose, glucose, sucrose, and magnesium carbonate, may beemployed. Biodegradable microspheres (e.g., polylactate polyglycolate)may also be employed as carriers for the pharmaceutical compositions ofthis invention. Suitable biodegradable microspheres are disclosed, forexample, in U.S. Pat. Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128;5,820,883; 5,853,763; 5,814,344 and 5,942,252. For certain topicalapplications, formulation as a cream or lotion, using well-knowncomponents, is preferred.

[0121] Such compositions may also comprise buffers (e.g., neutralbuffered saline or phosphate buffered saline), carbohydrates (e.g.,glucose, mannose, sucrose or dextrans), mannitol, proteins, peptides oramino acids such as glycine, antioxidants, bacteriostats, chelatingagents such as EDTA or glutathione, adjuvants (e.g., aluminumhydroxide), solutes that render the formulation isotonic, hypotonic orweakly hypertonic with the blood of a recipient, suspending agents,thickening agents and/or preservatives. Alternatively, compositions ofthe present invention may be formulated as a lyophilizate, or formulatedwith one or more liposomes, microspheres, nanoparticles, or micronizeddelivery systems using well-known technology.

[0122] Any of a variety of immunostimulants, such as adjuvants, may beemployed in the preparation of vaccine compositions of this invention.Most adjuvants contain a substance designed to protect the antigen fromrapid catabolism, such as aluminum hydroxide or mineral oil, and astimulator of immune responses, such as lipid A, Bortadella pertussis orMycobacterium tuberculosis derived proteins. Suitable adjuvants arecommercially available as, for example, alum-based adjuvants (e.g.,Alhydrogel, Rehydragel, aluminum phosphate, Algammulin, aluminumhydroxide); oil based adjuvants (Freund's Incomplete Adjuvant andComplete Adjuvant (Difco Laboratories, Detroit, Mich.), Specol, RIBI,TiterMax, Montanide ISA50 or Seppic MONTANIDE ISA 720); nonionic blockcopolymer-based adjuvants, cytokines (e.g., GM-CSF or Flat3-ligand);Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2(SmithKline Beecham, Philadelphia, Pa.); salts of calcium, iron or zinc;an insoluble suspension of acylated tyrosine; acylated sugars;cationically or anionically derivatized polysaccharides;polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A andQuil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, may alsobe used as adjuvants.

[0123] Hemocyanins and hemoerythrins may also be used in the invention.The use of hemocyanin from keyhole limpet (KLH) is particularlypreferred, although other molluscan and arthropod hemocyanins andhemoerythrins may be employed. Various polysaccharide adjuvants may alsobe used. Polyamine varieties of polysaccharides are particularlypreferred, such as chitin and chitosan, including deacetylated chitin.

[0124] A further preferred group of adjuvants are the muramyl dipeptide(MDP, N-acetylmuramyl-L-alanyl-D-isoglutamine) group of bacterialpeptidoglycans. Derivatives of muramyl dipeptide, such as the amino acidderivative threonyl-MDP, and the fatty acid derivative MTPPE, are alsocontemplated.

[0125] U.S. Pat. No. 4,950,645 describes a lipophilicdisaccharide-tripeptide derivative of muramyl dipeptide that is proposedfor use in artificial liposomes formed from phosphatidyl choline andphosphatidyl glycerol. It is said to be effective in activating humanmonocytes and destroying tumor cells, but is non-toxic in generally highdoses. The compounds of U.S. Pat. No. 4,950,645, and Intl. Pat. Appl.Publ. No. WO 91/16347 are also proposed for use in achieving particularaspects of the present invention.

[0126] BCG and BCG-cell wall skeleton (CWS) may also be used asadjuvants in the invention, with or without trehalose dimycolate.Trehalose dimycolate may be used itself. Azuma et al. (1988) show thattrehalose dimycolate administration correlates with augmented resistanceto influenza virus infection in mice. Trehalose dimycolate may beprepared as described in U.S. Pat. No. 4,579,945.

[0127] Amphipathic and surface-active agents, e.g., saponin andderivatives such as QS21 (Cambridge Biotech), form yet another group ofpreferred adjuvants for use with the immunogens of the presentinvention. Nonionic block copolymer surfactants (Rabinovich et al.,1994; Hunter et al., 1991) may also be employed. Oligonucleotides, asdescribed by Yamamoto et al. (1988) are another useful group ofadjuvants. Quil A and lentinen are also preferred adjuvants.

[0128] Superantigens are also contemplated for use as adjuvants in thepresent invention. “Superantigens” are generally bacterial products thatstimulate a greater proportion of T lymphocytes than peptide antigenswithout a requirement for antigen processing (Mooney et. al., 1994).Superantigens include Staphylococcus exoproteins, such as the α, β, γand δ enterotoxins from S. aureus and S. epidermidis, and the α, β, γand δ E. coli exotoxins.

[0129] Common Staphylococcus enterotoxins are known as staphylococcalenterotoxin A (SEA) and staphylococcal enterotoxin B (SEB), withenterotoxins through E (SEE) being described (Rott et. al., 1992).Streptococcus pyogenes B (SEB), Clostridium perfringens enterotoxin(Bowness et. al., 1992), cytoplasmic membrane-associated protein (CAP)from S. pyogenes (Sato et. al., 1994) and toxic shock syndrome toxin-i(TSST-1) from S. aureus (Schwab et. al., 1993) are further usefulsuperantigens.

[0130] One group of adjuvants particularly preferred for use in theinvention are the detoxified endotoxins, such as the refined detoxifiedendotoxin of U.S. Pat. No. 4,866,034. These refined detoxifiedendotoxins are effective in producing adjuvant responses in mammals.

[0131] The detoxified endotoxins may be combined with other adjuvants.Combination of detoxified endotoxins with trehalose dimycolate iscontemplated, as described in U.S. Pat. No. 4,435,386. Combinations ofdetoxified endotoxins with trehalose dimycolate and endotoxicglycolipids is also contemplated (U.S. Pat. No. 4,505,899), as iscombination of detoxified endotoxins with cell wall skeleton (CWS) orCWS and trehalose dimycolate, as described in U.S. Pat. Nos. 4,436,727,4,436,728 and 4,505,900. Combinations of just CWS and trehalosedimycolate, without detoxified endotoxins are also envisioned to beuseful, as described in U.S. Pat. No. 4,520,019.

[0132] MPL is currently one preferred immunopotentiating agent for useherein. References that concern the uses of MPL include Tomai et al.(1987), Chen et al. (1991) and Garg and Subbarao (1992), that eachconcern certain roles of MPL in the reactions of aging mice; Elliott etal. (1991), that concerns the D-galactosamine loaded mouse and itsenhanced sensitivity to lipopolysaccharide and MPL; Chase et al. (1986),that relates to bacterial infections; and Masihi et al. (1988), thatdescribes the effects of MPL and endotoxin on resistance of mice toToxoplasma gondii. Fitzgerald (1991) also reported on the use of MPL toup-regulate the immunogenicty of a syphilis vaccine and to confersignificant protection against challenge infection in rabbits.

[0133] Thus MPL is known to be safe for use, as shown in the above modelsystems. Phase-I clinical trials have also shown MPL to be safe for use(Vosika et al., 1984). Indeed, 100 μg/m² is known to be safe for humanuse, even on an outpatient basis (Vosika et al., 1984).

[0134] MPL generally induces polyclonal B cell activation (Baker et al.,1994), and has been shown to augment antibody production in manysystems, for example, in immunologically immature mice (Baker et al.,1988); in aging mice (Tomai and Johnson, 1989); and in nude and Xid mice(Madonna and Vogel, 1986; Myers et al., 1995). Antibody production hasbeen shown against erythrocytes (Hraba et al., 1993); T cell dependentand independent antigens; Pnu-immune vaccine (Garg and Subbarao, 1992);isolated tumor-associated antigens (U.S. Pat. No. 4,877,611); againstsyngeneic tumor cells (Livingston et al., 1985; Ravindranath et al.,1994a;b); and against tumor-associated gangliosides (Ravindranath etal., 1994a;b).

[0135] Another useful attribute of MPL is that is augments IgMresponses, as shown by Baker et al. (1988a), who describe the ability ofMPL to increase antibody responses in young mice. This is a particularlyuseful feature of an adjuvant for use in certain embodiments of thepresent invention. Myers et al. (1995) recently reported on the abilityof MPL to induce IgM antibodies, by virtue T cell-independent antibodyproduction.

[0136] In the Myers et al. (1995) studies, MPL was conjugated to thehapten, TNP. MPL was proposed for use as a carrier for other haptens,such as peptides.

[0137] MPL also activates and recruits macrophages (Verma et al., 1992).Tomai and Johnson (1989) showed that MPL-stimulated T cells enhance IL-1secretion by macrophages. MPL is also known to activate superoxideproduction, lysozyme activity, phagocytosis, and killing of Candida inmurine peritoneal macrophages (Chen et al., 1991).

[0138] The effects of MPL on T cells include the endogenous productionof cytotoxic factors, such as TNF, in serum of BCG-primed mice by MPL(Bennett et al., 1988). Kovach et al. (1990) and Elliot et al. (1991)also show that MPL induces TNF activity. MPL is known to act with TNF-αto induce release of IFN-γ by NK cells. IFN-γ production by T cells inresponse to MPL was also documented by Tomai and Johnson (1989), andOdean et al. (1990).

[0139] MPL is also known to be a potent T cell adjuvant. For example,MPL stimulates proliferation of melanoma-antigen specific CTLs (Mitchellet al., 1988, 1993). Further, Baker et al. (1988b) showed that nontoxicMPL inactivated suppressor T cell activity. Naturally, in thephysiological environment, the inactivation of T suppressor cells allowsfor increased benefit for the animal, as realized by, e.g., increasedantibody production. Johnson and Tomai (1988) have reported on thepossible cellular and molecular mediators of the adjuvant action of MPL.

[0140] MPL is also known to induce aggregation of platelets and tophosphorylate a platelet protein prior to induction of serotoninsecretion (Grabarek et al., 1990). This study shows that MPL is involvedin protein kinase C activation and signal transduction.

[0141] Many articles concern the structure and function of MPL include.These include Johnson et al. (1990), that describes the structuralcharacterization of MPL homologs obtained from Salmonella minnesotaRe595 lipopolysaccharide. The work of Johnson et al. (1990), in commonwith Grabarek et al. (1990), shows that the fatty acid moieties of MPLcan vary, even in commercial species. In separating MPL into eightfractions by thin layer chromatography, Johnson et al. (1990) found thatthree were particularly active, as assessed using human plateletresponses. The chemical components of the various MPL species werecharacterized by Johnson et al. (1990).

[0142] Baker et al. (1992) further analyzed the structural features thatinfluence the ability of lipid A and its analogs to abolish expressionof suppressor T cell activity. They reported that decreasing the numberof phosphate groups in lipid A from two to one (i.e., creatingmonophosphoryl lipid A, MPL) as well as decreasing the fatty acylcontent, primarily by removing the residue at the 3 position, resultedin a progressive reduction in toxicity; however, these structuralmodifications did not influence its ability to abolish the expression ofTs function (Baker et al., 1992). These types of MPL are ideal for usein the present invention.

[0143] Baker et al. (1992) also showed that reducing the fatty acylcontent from five to four (lipid A precursor IV_(A) or I_(a)) eliminatedthe capacity to influence Ts function but not to induce polyclonalactivation of B cells. These studies show that in order to be able toabolish the expression of Ts function, lipid A must be a glucosaminedisaccharide; may have either one or two phosphate groups; and must haveat least five fatty acyl groups. Also, the chain length of thenonhydroxylated fatty acid, as well as the location of acyloxyacylgroups (2′ versus 3′ position), may play an important role (Baker etal., 1992).

[0144] In examining the relationship between chain length and positionof fatty acyl groups on the ability of lipid A to abolish the expressionof suppressor T-cell (Ts) activity, Baker et al. (1994) found that fattyacyl chain lengths of C₁₂ to C₁₄ appeared to be optimal for bioactivity.Therefore, although their use is still possible, lipid A preparationswith fatty acyl groups of relatively short chain length (C₁₀ to C₁₂ fromPseudomonas aeruginosa and Chromobacterium violaceum) or predominantlylong chain length (C₁₈ from Helicobacter pylori) are less preferred foruse in this invention.

[0145] Baker et al. (1994) also showed that the lipid A proximal innercore region oligosaccharides of some bacterial lipopolysaccharidesincrease the expression of Ts activity; due mainly to the capacity ofsuch oligosaccharides, which are relatively conserved in structure amonggram-negative bacterial, to enlarge or expand upon the population ofCD8⁺ Ts generated during the course of a normal antibody response tounrelated microbial antigens. The minimal structure required for theexpression of the added immunosuppression observed was reported to be ahexasaccharide containing one 2-keto-3-deoxyoctonate residue, twoglucose residues, and three heptose residues to which are attached twopyrophosphorylethanolamine groups (Baker et al., 1994). This informationmay be considered in utilizing or even designing further adjuvants foruse in the invention.

[0146] In a generally related line of work, Tanamoto et al. (1994a;b;1995) described the dissociation of endotoxic activities in a chemicallysynthesized Lipid A precursor after acetylation or succinylation. Thus,compounds such as “acetyl 406” and “succinyl 516” (Tanamoto et al.,1994a;b; 1995) are also contemplated for use in the invention.

[0147] Synthetic MPLs form a particularly preferred group of antigens.For example, Brade et al. (1993) described an artificial glycoconjugatecontaining the bisphosphorylated glucosamine disaccharide backbone oflipid A that binds to anti-Lipid A MAbs. This is one candidate for usein certain aspects of the invention.

[0148] The MPL derivatives described in U.S. Pat. No. 4,987,237 areparticularly contemplated for use in the present invention. U.S. Pat.No. 4,987,237 describes MPL derivatives that contain one or more freegroups, such as amines, on a side chain attached to the primary hydroxylgroups of the monophosphoryl lipid A nucleus through an ester group. Thederivatives provide a convenient method for coupling the lipid A throughcoupling agents to various biologically active materials. Theimmunostimulant properties of lipid A are maintained. All MPLderivatives in accordance with U.S. Pat. No. 4,987,237 are envisionedfor use in the MPL adjuvant-incorporated cells of this invention.

[0149] Various adjuvants, even those that are not commonly used inhumans, may still be employed in animals, where, for example, onedesires to raise antibodies or to subsequently obtain activated T cells.The toxicity or other adverse effects that may result from either theadjuvant or the cells, e.g., as may occur using non-irradiated tumorcells, is irrelevant in such circumstances.

[0150] Within the vaccines provided herein, the adjuvant composition ispreferably designed to induce an immune response predominantly of theTh1 type. High levels of Th1-type cytokines (e.g., IFN-γ, TNFα, IL-2 andIL-12) tend to favor the induction of cell-mediated immune responses toan administered antigen. In contrast, high levels of Th2-type cytokines(e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction ofhumoral immune responses. Following application of a vaccine as providedherein, a patient will support an immune response that includes Th1- andTh2-type responses. Within a preferred embodiment, in which a responseis predominantly Th1-type, the level of Th1-type cytokines will increaseto a greater extent than the level of Th2-type cytokines. The levels ofthese cytokines may be readily assessed using standard assays. For areview of the families of cytokines see e.g., Mosmann and Coffman(1989).

[0151] Preferred adjuvants for use in eliciting a predominantly Th1-typeresponse include, for example, a combination of monophosphoryl lipid A,preferably 3-de-O-acylated mono-phosphoryl lipid A (3D-MPL), togetherwith an aluminum salt. MPL adjuvants are available from CorixaCorporation (Seattle, Wash.; see e.g., U.S. Pat. Nos. 4,436,727;4,877,611; 4,866,034 and 4,912,094, each of which is specificallyincorporated herein by reference in its entirety). CpG-containingoligonucleotides (in which the CpG dinucleotide is unmethylated) alsoinduce a predominantly Th1 response. Such oligonucleotides are wellknown and are described, for example, in Intl. Pat. Appl. Publ. No. WO96/02555 and Intl. Pat. Appl. Publ. No. WO 99/33488. ImmunostimulatoryDNA sequences are also described, for example, by Sato et al. (1996).Another preferred adjuvant is a saponin, preferably QS21 (AquilaBiopharmaceuticals Inc., Framingham, Mass.), which may be used alone orin combination with other adjuvants. For example, an enhanced systeminvolves the combination of a monophosphoryl lipid A and saponinderivative, such as the combination of QS21 and 3D-MPL (see e.g., Intl.Pat. Appl. Publ. No. WO 94/00153), or a less reactogenic compositionwhere the QS21 is quenched with cholesterol (see e.g., Intl. Pat. Appl.Publ. No. WO 96/33739). Other preferred formulations comprise anoil-in-water emulsion and tocopherol. A particularly potent adjuvantformulation involving QS21, 3D-MPL and tocopherol in an oil-in-wateremulsion has also been described (see e.g., Intl. Pat. Appl. Publ. No.WO 95/17210).

[0152] Other preferred adjuvants include Montanide ISA 720 (Seppic), SAF(Chiron), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants(e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart,Belgium), Detox (Corixa Corporation), RC-529 (Corixa Corporation) andaminoalkyl glucosaminide 4-phosphates (AGPs).

[0153] Any vaccine provided herein may be prepared using well-knownmethods that result in a combination of one or more antigens, one ormore immunostimulants or adjuvants and one or more suitable carriers,excipients, or pharmaceutically acceptable buffers. The compositionsdescribed herein may be administered as part of a sustained releaseformulation (i.e., a formulation such as a capsule, sponge or gel[composed of polysaccharides, for example] that effects a slow releaseof compound following administration). Such formulations may generallybe prepared using well-known technology (Coombes et al., 1996) andadministered by, for example, oral, rectal or subcutaneous implantation,or by implantation at the desired target site. Sustained-releaseformulations may contain a peptide, polynucleotide or antibody dispersedin a carrier matrix and/or contained within a reservoir surrounded by arate-controlling membrane.

[0154] Carriers for use within such formulations are preferablybiocompatible, and may also be biodegradable; preferably the formulationprovides a relatively constant level of active component release. Suchcarriers include microparticles of poly(lactide-co-glycolide), as wellas polyacrylate, latex, starch, cellulose and dextran. Otherdelayed-release carriers include supramolecular biovectors, whichcomprise a non-liquid hydrophilic core (e.g., a cross-linkedpolysaccharide or oligosaccharide) and, optionally, an external layercomprising an amphiphilic compound, such as a phospholipid (U.S. Pat.No. 5,151,254; Intl. Pat. Appl. Publ. No. WO 94/20078; Intl. Pat. Appl.Publ. No. WO/94/23701; and Intl. Pat. Appl. Publ. No. WO 96/06638). Theamount of active compound contained within a sustained releaseformulation depends upon the site of implantation, the rate and expectedduration of release and the nature of the condition to be treated orprevented.

[0155] Any of a variety of delivery vehicles may be employed withinpharmaceutical compositions and vaccines to facilitate production of anantigen-specific immune response that targets tumor cells. Deliveryvehicles include antigen-presenting cells (APCs), such as dendriticcells, macrophages, B cells, monocytes and other cells that may beengineered to be efficient APCs. Such cells may, but need not, begenetically modified to increase the capacity for presenting theantigen, to improve activation and/or maintenance of the T cellresponse, to have anti-tumor effects per se and/or to be immunologicallycompatible with the receiver (i.e., matched HLA haplotype). APCs maygenerally be isolated from any of a variety of biological fluids andorgans, including tumor and peritumoral tissues, and may be autologous,allogeneic, syngeneic or xenogeneic cells.

[0156] Certain preferred embodiments of the present invention usedendritic cells or progenitors thereof as antigen-presenting cells.Dendritic cells are highly potent APCs (Banchereau and Steinman, 1998)and have been shown to be effective as a physiological adjuvant foreliciting prophylactic or therapeutic antitumor immunity (Timmerman andLevy, 1999). In general, dendritic cells may be identified based ontheir typical shape (stellate in situ, with marked cytoplasmic processes(dendrites) visible in vitro), their ability to take up, process andpresent antigens with high efficiency and their ability to activatenaive T cell responses. Dendritic cells may, of course, be engineered toexpress specific cell-surface receptors or ligands that are not commonlyfound on dendritic cells in vivo or ex vivo, and such modified dendriticcells are contemplated by the present invention. As an alternative todendritic cells, secreted vesicles antigen-loaded dendritic cells(called exosomes) may be used within a vaccine (Zitvogel et al., 1998).

[0157] Dendritic cells and progenitors may be obtained from peripheralblood, bone marrow, tumor-infiltrating cells, peritumoraltissues-infiltrating cells, lymph nodes, spleen, skin, umbilical cordblood or any other suitable tissue or fluid. For example, dendriticcells may be differentiated ex vivo by adding a combination of cytokinessuch as GM-CSF, IL-4, IL-13 and/or TNFα to cultures of monocytesharvested from peripheral blood. Alternatively, CD34 positive cellsharvested from peripheral blood, umbilical cord blood or bone marrow maybe differentiated into dendritic cells by adding to the culture mediumcombinations of GM-CSF, IL-3, TNFα, CD40 ligand, LPS, flt3 ligand and/orother compound(s) that induce differentiation, maturation andproliferation of dendritic cells.

[0158] Dendritic cells are conveniently categorized as “immature” and“mature” cells, which allows a simple way to discriminate between twowell characterized phenotypes. However, this nomenclature should not beconstrued to exclude all possible intermediate stages ofdifferentiation. Immature dendritic cells are characterized as APC witha high capacity for antigen uptake and processing, which correlates withthe high expression of Fcy receptor and mannose receptor. The maturephenotype is typically characterized by a lower expression of thesemarkers, but a high expression of cell surface molecules responsible forT cell activation such as class I and class II MHC, adhesion molecules(e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80,CD86 and 4-1BB).

[0159] APCs may generally be transfected with a polynucleotide encodinga hematological malignancy related peptide, such that the peptide, or animmunogenic portion thereof, is expressed on the cell surface. Suchtransfection may take place ex vivo, and a composition or vaccinecomprising such transfected cells may then be used for therapeuticpurposes, as described herein. Alternatively, a gene delivery vehiclethat targets a dendritic or other antigen-presenting cell may beadministered to a patient, resulting in transfection that occurs invivo. In vivo and ex vivo transfection of dendritic cells, for example,may generally be performed using any methods known in the art, such asthose described in Intl. Pat. Appl. Publ. No. WO 97/24447, or the genegun approach described by Mahvi et al. (1997). Antigen loading ofdendritic cells may be achieved by incubating dendritic cells orprogenitor cells with the hematological malignancy related peptide, DNA(naked or within a plasmid vector) or RNA; or with antigen-expressingrecombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus orlentivirus vectors). Prior to loading, the peptide may be covalentlyconjugated to an immunological partner that provides T cell help (e.g.,a carrier molecule). Alternatively, a dendritic cell may be pulsed witha non-conjugated immunological partner, separately or in the presence ofthe peptide.

[0160] Combined therapeutics is also contemplated, and the same type ofunderlying pharmaceutical compositions may be employed for both singleand combined medicaments. Vaccines and pharmaceutical compositions maybe presented in unit-dose or multi-dose containers, such as sealedampoules or vials. Such containers are preferably hermetically sealed topreserve sterility of the formulation until use. In general,formulations may be stored as suspensions, solutions or emulsions inoily or aqueous vehicles. Alternatively, a vaccine or pharmaceuticalcomposition may be stored in a freeze-dried condition requiring only theaddition of a sterile liquid carrier immediately prior to use.

[0161] 4.5 Diagnostic and Prognostic Methods for HematologicalMalignancy Diseases

[0162] The present invention further provides methods for detecting amalignant disease associated with one or more of the polypeptide orpolynucleotide compositions disclosed herein, and for monitoring theeffectiveness of an immunization or therapy for such a disease. Todetermine the presence or absence of a malignant disease associated withone or more of the polypeptide or polynucleotide compositions disclosedherein, a patient may be tested for the level of T cells specific forone or more of such compositions. Within certain methods, a biologicalsample comprising CD4⁺ and/or CD⁸⁺ T cells isolated from a patient isincubated with one or more of the polypeptide or polynucleotidecompositions disclosed herein, and/or an APC that expresses one or moreof such peptides or polypeptides, and the presence or absence ofspecific activation of the T cells is detected, as described herein.Suitable biological samples include, but are not limited to, isolated Tcells. For example, T cells may be isolated from a patient by routinetechniques (such as by Ficoll/Hypaque density gradient centrifugation ofperipheral blood lymphocytes). T cells may be incubated in vitro for 2-9days (typically 4 days) at 37° C. with one or more of the disclosedpeptide, polypeptide or polynucleotide compositions (e.g., 5-25 μg/ml).It may be desirable to incubate another aliquot of a T cell sample inthe absence of the composition to serve as a control. For CD4⁺ T cells,activation is preferably detected by evaluating proliferation of the Tcells. For CD8⁺ T cells, activation is preferably detected by evaluatingcytolytic activity. A level of proliferation that is at least two foldgreater and/or a level of cytolytic activity that is at least 20%greater than in disease-free patients indicates the presence of amalignant disease associated with expression or one or more of thedisclosed polypeptide or polynucleotide compositions. Furthercorrelation may be made, using methods well known in the art, betweenthe level of proliferation and/or cytolytic activity and the predictedresponse to therapy. In particular, patients that display a higherantibody, proliferative and/or lytic response may be expected to show agreater response to therapy.

[0163] Within other methods, a biological sample obtained from a patientis tested for the level of antibody specific for one or more of thehematological malignancy-related peptides or polypeptide s disclosedherein. The biological sample is incubated with hematologicalmalignancy-related peptide or polypeptide, or a polynucleotide encodingsuch a peptide or polypeptide, and/or an APC that expresses such apeptide or polypeptide under conditions and for a time sufficient toallow immunocomplexes to form. Immunocomplexes formed between theselected peptide or polypeptide and antibodies in the biological samplethat specifically bind to the selected peptide or polypeptide are thendetected. A biological sample for use within such methods may be anysample obtained from a patient that would be expected to containantibodies. Suitable biological samples include blood, sera, ascites,bone marrow, pleural effusion, and cerebrospinal fluid.

[0164] The biological sample is incubated with the selected peptide orpolypeptide in a reaction mixture under conditions and for a timesufficient to permit immunocomplexes to form between the selectedpeptide or polypeptide and antibodies that are immunospecific for such apeptide or polypeptide. For example, a biological sample and a selectedpeptide or polypeptide peptide may be incubated at 4° C. for 24-48 hrs.

[0165] Following the incubation, the reaction mixture is tested for thepresence of immuno-complexes. Detection of immunocomplexes formedbetween the selected peptide or polypeptide and antibodies present inthe biological sample may be accomplished by a variety of knowntechniques, such as radioimmunoassays (RIA) and enzyme linkedimmunosorbent assays (ELISA). Suitable assays are well known in the artand are amply described in the scientific and patent literature (Harlowand Lane, 1988). Assays that may be used include, but are not limitedto, the double monoclonal antibody sandwich immunoassay technique (U.S.Pat. No. 4,376,110); monoclonal-polyclonal antibody sandwich assays(Wide et al., 1970); the “western blot” method (U.S. Pat. No.4,452,901); immunoprecipitation of labeled ligand (Brown et al., 1980);enzyme-linked immunosorbent assays (Raines and Ross, 1982);immunocytochemical techniques, including the use of fluorochromes(Brooks et al., 1980); and neutralization of activity (Bowen-Pope etal., 1984). Other immunoassays include, but are not limited to, thosedescribed in U.S. Pat. Nos. 3,817,827; 3,850,752; 3,901,654; 3,935,074;3,984,533; 3,996,345; 4,034,074; and 4,098,876.

[0166] For detection purposes, the selected peptide or polypeptide mayeither be labeled or unlabeled. Unlabeled polypeptide peptide may beused in agglutination assays or in combination with labeled detectionreagents that bind to the immunocomplexes (e.g., anti-immunoglobulin,protein G, Protein A or a lectin and secondary antibodies, orantigen-binding fragments thereof, capable of binding to the antibodiesthat specifically bind to the selected hematological malignancy-relatedpeptide or polypeptide). If the selected peptide or polypeptide islabeled, the reporter group may be any suitable reporter group known inthe art, including radioisotopes, fluorescent groups, luminescentgroups, enzymes, biotin and dye particles.

[0167] Within certain assays, unlabeled peptide or polypeptide isimmobilized on a solid support. The solid support may be any materialknown to those of ordinary skill in the art to which the peptide may beattached. For example, the solid support may be a test well in amicrotiter plate or a nitrocellulose or other suitable membrane.Alternatively, the support may be a bead or disc, such as glass,fiberglass, latex or a plastic material such as polystyrene orpolyvinylchloride. The support may also be a magnetic particle or afiber optic sensor, such as those disclosed, for example, in U.S. Pat.No. 5,359,681. The peptide may be immobilized on the solid support usinga variety of techniques known to those of skill in the art, which areamply described in the patent and scientific literature. In the contextof the present invention, the term “immobilization” refers to bothnoncovalent association, such as adsorption, and covalent attachment(which may be a direct linkage between the antigen and functional groupson the support or may be a linkage by way of a cross-linking agent).Immobilization by adsorption to a well in a microtiter plate or to amembrane is preferred. In such cases, adsorption may be achieved bycontacting the selected peptide or polypeptide, in a suitable buffer,with the solid support for a suitable amount of time. The contact timevaries with temperature, but is typically between about 1 hour and about1 day. In general, contacting a well of a plastic microtiter plate (suchas polystyrene or polyvinylchloride) with an amount of peptide rangingfrom about 10 ng to about 10 μg, and preferably about 100 ng to about 1μg, is sufficient to immobilize an adequate amount of peptide.

[0168] Following immobilization, the remaining protein binding sites onthe support are typically blocked. Any suitable blocking agent known tothose of ordinary skill in the art, such as bovine serum albumin, Tween™20™ (Sigma Chemical Co., St. Louis, Mo.), heat-inactivated normal goatserum (NGS), or BLOTTO (buffered solution of nonfat dry milk which alsocontains a preservative, salts, and an antifoaming agent) may be used.The support is then incubated with a biological sample suspected ofcontaining specific antibody. The sample can be applied neat, or, moreoften, it can be diluted, usually in a buffered solution which containsa small amount (0.1%-5.0% by weight) of protein, such as BSA, NGS, orBLOTTO. In general, an appropriate contact time (i.e., incubation time)is a period of time that is sufficient to detect the presence ofantibody or an antigen binding fragment that is immunospecific for theselected peptide or polypeptide within a sample containing such anantibody or binding fragment thereof. Preferably, the contact time issufficient to achieve a level of binding that is at least about 95% ofthat achieved at equilibrium between bound and unbound antibody orantibody fragment. Those of ordinary skill in the art will recognizethat the time necessary to achieve equilibrium may be readily determinedby assaying the level of binding that occurs over a period of time. Atroom temperature, an incubation time of about 30 min is generallysufficient.

[0169] Unbound sample may then be removed by washing the solid supportwith an appropriate buffer, such as PBS containing 0.1% Tween™ 20. Adetection reagent that binds to the immunocomplexes and that comprisesat least a first detectable label or “reporter” molecule may then beadded. The detection reagent is incubated with the immunocomplex for anamount of time sufficient to detect the bound antibody or antigenbinding fragment thereof. An appropriate amount of time may generally bedetermined by assaying the level of binding that occurs over a period oftime. Unbound label or detection reagent is then removed and bound labelor detection reagent is detected using a suitable assay or analyticalinstrument. The method employed for detecting the reporter group dependsupon the nature of the reporter group. For radioactive labels,scintillation counting or autoradiographic methods are generallyappropriate. Spectroscopic methods may be used to detect dyes,luminescent or chemiluminescent moieties and various chromogens,fluorescent labels and such like. Biotin may be detected using avidin,coupled to a different reporter group (commonly a radioactive orfluorescent group or an enzyme). Enzyme reporter groups (e.g.,horseradish peroxidase, β-galactosidase, alkaline phosphatase andglucose oxidase) may generally be detected by the addition of substrate(generally for a specific period of time), followed by spectroscopic orother analysis of the reaction products. Regardless of the specificmethod employed, a level of bound detection reagent that is at least twofold greater than background (i.e., the level observed for a biologicalsample obtained from a disease-free individual) indicates the presenceof a malignant disease associated with expression of the selectedpeptide or polypeptide.

[0170] In general, methods for monitoring the effectiveness of animmunization or therapy involve monitoring changes in the level ofantibodies or T cells specific for the selected peptide or polypeptidein a sample, or in an animal such as a human patient. Methods in whichantibody levels are monitored may comprise the steps of: (a) incubatinga first biological sample, obtained from a patient prior to a therapy orimmunization, with a selected peptide or polypeptide, wherein theincubation is performed under conditions and for a time sufficient toallow immunocomplexes to form; (b) detecting immunocomplexes formedbetween the selected peptide or polypeptide and antibodies or antigenbinding fragments in the biological sample that specifically bind to theselected peptide or polypeptide; (c) repeating steps (a) and (b) using asecond biological sample taken from the patient at later time, such asfor example, following a given therapy or immunization; and (d)comparing the number of immunocomplexes detected in the first and secondbiological samples. Alternatively, a polynucleotide encoding theselected peptide or polypeptide, or an APC expressing the selectedpeptide or polypeptide may be employed in place of the selected peptideor polypeptide itself. Within such methods, immunocomplexes between theselected peptide or polypeptide encoded by a polynucleotide, orexpressed by the APC, and antibodies and/or antigen binding fragments inthe biological sample are detected.

[0171] Methods in which T cell activation and/or the number ofhematological malignancy polypeptide-specific precursors are monitoredmay comprise the steps of: (a) incubating a first biological samplecomprising CD4⁺ and/or CD8⁺ cells (e.g., bone marrow, peripheral bloodor a fraction thereof), obtained from a patient prior to a therapy orimmunization, with a hematological malignancy peptide or polypeptide,wherein the incubation is performed under conditions and for a timesufficient to allow specific activation, proliferation and/or lysis of Tcells; (b) detecting an amount of activation, proliferation and/or lysisof the T cells; (c) repeating steps (a) and (b) using a secondbiological sample comprising CD4⁺ and/or CD8⁺ T cells, and taken fromthe same patient following therapy or immunization; and (d) comparingthe amount of activation, proliferation and/or lysis of T cells in thefirst and second biological samples. Alternatively, a polynucleotideencoding a hematological malignancy related peptide, or an APCexpressing such a peptide may be employed in place of the hematologicalmalignancy peptide itself.

[0172] A biological sample for use within such methods may be any sampleobtained from a patient that would be expected to contain antibodies,CD4⁺ T cells and/or CD8⁺ T cells. Suitable biological samples includeblood, sera, ascites, bone marrow, pleural effusion and cerebrospinalfluid. A first biological sample may be obtained prior to initiation oftherapy or immunization or part way through a therapy or vaccinationregime. The second biological sample should be obtained in a similarmanner, but at a time following additional therapy or immunization. Thesecond biological sample may be obtained at the completion of, or partway through, therapy or immunization, provided that at least a portionof therapy or immunization takes place between the isolation of thefirst and second biological samples.

[0173] Incubation and detection steps for both samples may generally beperformed as described above. A statistically significant increase inthe number of immunocomplexes in the second sample relative to the firstsample reflects successful therapy or immunization.

[0174] 4.6 Administration of Pharmaceutical Compositions andFormulations

[0175] In certain embodiments, the present invention concernsformulation of one or more of the polynucleotide, polypeptide, peptide,antibody, or antigen binding fragment compositions disclosed herein inpharmaceutically acceptable solutions for administration to a cell or ananimal, either alone, or in combination with one or more othermodalities of anti-cancer therapy, or in combination with one or morediagnostic or therapeutic agents.

[0176] It will also be understood that, if desired, the nucleic acidsegment, RNA, or DNA compositions disclosed herein may be administeredin combination with other agents as well, such as, e.g., proteins orpeptides or various pharmaceutically-active agents. As long as thecomposition comprises at least one of the genetic expression constructsdisclosed herein, there is virtually no limit to other components thatmay also be included, given that the additional agents do not cause asignificant adverse effect upon contact with the target cells or hosttissues. The RNA- or DNA-derived compositions may thus be deliveredalong with various other agents as required in the particular instance.Such RNA or DNA compositions may be purified from host cells or otherbiological sources, or alternatively may be chemically synthesized asdescribed herein. Likewise, such compositions may comprise substitutedor derivatized RNA or DNA compositions. Such compositions may includeone or more therapeutic gene constructs, either alone, or in combinationwith one or more modified peptide or nucleic acid substituentderivatives, and/or other anticancer therapeutics.

[0177] The formulation of pharmaceutically-acceptable excipients andcarrier solutions are well-known to those of skill in the art, as is thedevelopment of suitable dosing and treatment regimens for using theparticular compositions described herein in a variety of treatmentregimens, including e.g., oral, intravenous, intranasal, transdermal,intraprostatic, intratumoral, and/or intramuscular administration andformulation.

[0178] 4.6.1 Injectable Delivery

[0179] For example, the pharmaceutical compositions disclosed herein maybe administered parenterally, intravenously, intramuscularly, or evenintraperitoneally as described in U.S. Pat. No. 5,543,158, U.S. Pat. No.5,641,515 and U.S. Pat. No. 5,399,363 (each specifically incorporatedherein by reference in its entirety). Solutions of the active compoundsas free-base or pharmacologically acceptable salts may be prepared inwater suitably mixed with a surfactant, such as hydroxypropylcellulose.Dispersions may also be prepared in glycerol, liquid polyethyleneglycols, and mixtures thereof and in oils. Under ordinary conditions ofstorage and use, these preparations contain a preservative to preventthe growth of microorganisms.

[0180] The pharmaceutical forms suitable for injectable use includesterile aqueous solutions or dispersions and sterile powders for theextemporaneous preparation of sterile injectable solutions ordispersions (U.S. Pat. No. 5,466,468, specifically incorporated hereinby reference in its entirety). In all cases the form must be sterile andmust be fluid to the extent that easy syringability exists. It must bestable under the conditions of manufacture and storage and must bepreserved against the contaminating action of microorganisms, such asbacteria and fungi. The carrier can be a solvent or dispersion mediumcontaining, for example, water, ethanol, polyol (e.g., glycerol,propylene glycol, and liquid polyethylene glycol, and the like),suitable mixtures thereof, and/or vegetable oils. Proper fluidity may bemaintained, for example, by the use of a coating, such as lecithin, bythe maintenance of the required particle size in the case of dispersionand by the use of surfactants. The prevention of the action ofmicroorganisms can be brought about by various antibacterial andantifungal agents, for example, parabens, chlorobutanol, phenol, sorbicacid, thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars or sodium chloride.Prolonged absorption of the injectable compositions can be brought aboutby the use in the compositions of agents delaying absorption, forexample, aluminum monostearate and gelatin.

[0181] For parenteral administration in an aqueous solution, forexample, the solution should be suitably buffered if necessary and theliquid diluent first rendered isotonic with sufficient saline orglucose. These particular aqueous solutions are especially suitable forintravenous, intramuscular, subcutaneous and intraperitonealadministration. In this connection, sterile aqueous media that can beemployed will be known to those of skill in the art in light of thepresent disclosure. For example, one dosage may be dissolved in 1 ml ofisotonic NaCl solution and either added to 1000 ml of hypodermoclysisfluid or injected at the proposed site of infusion, (see for example,Hoover, 1975). Some variation in dosage will necessarily occur dependingon the condition of the subject being treated. The person responsiblefor administration will, in any event, determine the appropriate dosefor the individual subject. Moreover, for human administration,preparations should meet sterility, pyrogenicity, and general safety andpurity standards as required by FDA Office of Biologics standards.

[0182] Sterile injectable solutions may be prepared by incorporating thegene therapy constructs in the required amount in the appropriatesolvent with several of the other ingredients enumerated above, asrequired, followed by filtered sterilization. Generally, dispersions areprepared by incorporating the various sterilized active ingredients intoa sterile vehicle which contains the basic dispersion medium and therequired other ingredients from those enumerated above. In the case ofsterile powders for the preparation of sterile injectable solutions, thepreferred methods of preparation are vacuum-drying and freeze-dryingtechniques which yield a powder of the active ingredient plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

[0183] The compositions disclosed herein may be formulated in a neutralor salt form. Pharmaceutically-acceptable salts, include the acidaddition salts and which are formed with inorganic acids such as, forexample, hydrochloric or phosphoric acids, or such organic acids asacetic, oxalic, tartaric, mandelic, and the like. Salts formed with thefree carboxyl groups can also be derived from inorganic bases such as,for example, sodium, potassium, ammonium, calcium, or ferric hydroxides,and such organic bases as isopropylamine, trimethylamine, histidine,procaine and the like. Upon formulation, solutions will be administeredin a manner compatible with the dosage formulation and in such amount asis therapeutically effective. The formulations are easily administeredin a variety of dosage forms such as injectable solutions, drug releasecapsules and the like.

[0184] As used herein, “carrier” includes any and all solvents,dispersion media, vehicles, coatings, diluents, antibacterial andantifungal agents, isotonic and absorption delaying agents, buffers,carrier solutions, suspensions, colloids, and the like. The use of suchmedia and agents for pharmaceutical active substances is well known inthe art. Except insofar as any conventional media or agent isincompatible with the active ingredient, its use in the therapeuticcompositions is contemplated. Supplementary active ingredients can alsobe incorporated into the compositions.

[0185] 4.6.2 Intranasal Delivery

[0186] One may use nasal solutions or sprays, aerosols or even inhalantsfor the treatment of hematological malignancies with one of more of thedisclosed peptides and polynucleotides. Nasal solutions are usuallyaqueous solutions designed for administration to the nasal passages indrops or sprays. Nasal solutions are prepared so that they are similarin many respects to nasal secretions, so that normal ciliary action ismaintained. Thus, the aqueous nasal solutions usually are isotonic andslightly buffered to maintain a pH of from about 5.5 to about 6.5. Inaddition, antimicrobial preservatives, similar to those used inophthalmic preparations, and appropriate drug stabilizers, if required,may be included in the formulation. Various commercial nasalpreparations are known.

[0187] Inhalations and inhalants are pharmaceutical preparationsdesigned for delivering a drug or compound into the respiratory tree ofa patient. A vapor or mist is administered and reaches the affectedarea, often to give relief from symptoms of bronchial and nasalcongestion. However, this route can also be employed to deliver agentsinto the systemic circulation. Inhalations may be administered by thenasal or oral respiratory routes. The administration of inhalationsolutions is only effective if the droplets are sufficiently fine anduniform in size so that the mist reaches the bronchioles.

[0188] Another group of products, also known as inhalations, andsometimes called insufflations, consists of finely powdered or liquiddrugs that are carried into the respiratory passages by the use ofspecial delivery systems, such as pharmaceutical aerosols, that hold asolution or suspension of the drug in a liquefied gas propellant. Whenreleased through a suitable valve and oral adapter, a metered does ofthe inhalation is propelled into the respiratory tract of the patient.

[0189] Particle size is of importance in the administration of this typeof preparation. It has been reported that the optimum particle size forpenetration into the pulmonary cavity is of the order of about 0.5 toabout 7 μm. Fine mists are produced by pressurized aerosols and hencetheir use in considered advantageous.

[0190] 4.6.3 Liposome-, Nanocapsule-, and Microparticle-MediatedDelivery

[0191] In certain embodiments, the inventors contemplate the use ofliposomes, nanocapsules, microparticles, microspheres, lipid particles,vesicles, and the like, for the introduction of the polynucleotidecompositions of the present invention into suitable host cells. Inparticular, the polynucleotide compositions of the present invention maybe formulated for delivery either encapsulated in a lipid particle, aliposome, a vesicle, a nanosphere, or a nanoparticle or the like.

[0192] Such formulations may be preferred for the introduction ofpharmaceutically acceptable formulations of the nucleic acids disclosedherein. The formation and use of liposomes is generally known to thoseof skill in the art (see for example, Couvreur et al., 1977; Couvreur,1988; Lasic, 1998; which describes the use of liposomes and nanocapsulesin the targeted antibiotic therapy for intracellular bacterialinfections and diseases). Recently, liposomes were developed withimproved serum stability and circulation half-lives (Gabizon andPapahadjopoulos, 1988; Allen and Choun, 1987; U.S. Pat. No. 5,741,516,specifically incorporated herein by reference in its entirety). Further,various methods of liposome and liposome like preparations as potentialdrug carriers have been reviewed (Takakura, 1998; Chandran et al., 1997;Margalit, 1995; U.S. Pat. No. 5,567,434; U.S. Pat. No. 5,552,157; U.S.Pat. No. 5,565,213; U.S. Pat. No. 5,738,868 and U.S. Pat. No. 5,795,587,each specifically incorporated herein by reference in its entirety).

[0193] Liposomes have been used successfully with a number of cell typesthat are normally resistant to transfection by other proceduresincluding T cell suspensions, primary hepatocyte cultures and PC 12cells (Renneisen et al., 1990; Muller et al., 1990). In addition,liposomes are free of the DNA length constraints that are typical ofviral-based delivery systems. Liposomes have been used effectively tointroduce genes, drugs (Heath and Martin, 1986; Heath et al., 1986;Balazsovits et al., 1989; Fresta and Puglisi, 1996), radiotherapeuticagents (Pikul et al., 1987), enzymes (Imaizumi et al., 1990a; Imaizumiet al., 1990b), viruses (Faller and Baltimore, 1984), transcriptionfactors and allosteric effectors (Nicolau and Gersonde, 1979) into avariety of cultured cell lines and animals. In addition, severalsuccessful clinical trails examining the effectiveness ofliposome-mediated drug delivery have been completed (Lopez-Berestein etal., 1985a; 1985b; Coune, 1988; Sculier et al., 1988). Furthermore,several studies suggest that the use of liposomes is not associated withautoimmune responses, toxicity or gonadal localization after systemicdelivery (Mori and Fukatsu, 1992).

[0194] Liposomes are formed from phospholipids that are dispersed in anaqueous medium and spontaneously form multilamellar concentric bilayervesicles (also termed multilamellar vesicles (MLVs). MLVs generally havediameters of from 25 nm to 4 μm. Sonication of MLVs results in theformation of small unilamellar vesicles (SUVs) with diameters in therange of 200 to 500 Å, containing an aqueous solution in the core.

[0195] Liposomes bear resemblance to cellular membranes and arecontemplated for use in connection with the present invention ascarriers for the peptide compositions. They are widely suitable as bothwater- and lipid-soluble substances can be entrapped, i.e. in theaqueous spaces and within the bilayer itself, respectively. It ispossible that the drug-bearing liposomes may even be employed forsite-specific delivery of active agents by selectively modifying theliposomal formulation.

[0196] In addition to the teachings of Couvreur et al. (1977; 1988), thefollowing information may be utilized in generating liposomalformulations. Phospholipids can form a variety of structures other thanliposomes when dispersed in water, depending on the molar ratio of lipidto water. At low ratios the liposome is the preferred structure. Thephysical characteristics of liposomes depend on pH, ionic strength andthe presence of divalent cations. Liposomes can show low permeability toionic and polar substances, but at elevated temperatures undergo a phasetransition which markedly alters their permeability. The phasetransition involves a change from a closely packed, ordered structure,known as the gel state, to a loosely packed, less-ordered structure,known as the fluid state. This occurs at a characteristicphase-transition temperature and results in an increase in permeabilityto ions, sugars, and drugs.

[0197] Alternatively, the invention provides for pharmaceuticallyacceptable nanocapsule formulations of the polynucleotide compositionsof the present invention. Nanocapsules can generally entrap compounds ina stable and reproducible way (Henry-Michelland et al., 1987;Quintanar-Guerrero et al., 1998; Douglas et al., 1987). To avoid sideeffects due to intracellular polymeric overloading, such ultrafineparticles (sized around 0.1 μm) should be designed using polymers ableto be degraded in vivo. Biodegradable polyalkyl-cyanoacrylatenanoparticles that meet these requirements are contemplated for use inthe present invention, and such particles may be are easily made, asdescribed (Couvreur et al., 1980; 1988; zur Muhlen et al., 1998; Zambauxet al. 1998; Pinto-Alphandry et al., 1995 and U.S. Pat. No. 5,145,684,specifically incorporated herein by reference in its entirety). Inparticular, methods of polynucleotide delivery to a target cell usingeither nanoparticles or nanospheres (Schwab et al., 1994; Truong-Le etal., 1998) are also particularly contemplated to be useful informulating the disclosed compositions for administration to an animal,and to a human in particular.

[0198] 4.7 Therapeutic Agents and Kits

[0199] The invention also provides one or more of the hematologicalmalignancy-related compositions formulated with one or morepharmaceutically acceptable excipients, carriers, diluents, adjuvants,and/or other components for use in the preparation of medicaments, ordiagnostic reagents, as well as various kits comprising one or more ofsuch compositions, medicaments, or formulations intended foradministration to an animal in need thereof, or for use in one or morediagnostic assays for identifying polynucleotides, polypeptides, and/orantibodies that are specific for one or more hematologicalmalignancy-related compounds as described herein. In addition to thedisclosed epitopes, antibodies and antigen binding fragments, antibody-or antigen binding fragment-encoding polynucleotides or additionalanticancer agents, polynucleotides, peptides, antigens, or othertherapeutic compounds as may be employed in the formulation ofparticular compositions and formulations disclosed herein, andparticularly in the preparation of anticancer agents oranti-hematological malignancies therapies for administration to theaffected mammal.

[0200] As such, preferred animals for administration of thepharmaceutical compositions disclosed herein include mammals, andparticularly humans. Other preferred animals include primates, sheep,goats, bovines, equines, porcines, lupines, canines, and felines, aswell as any other mammalian species commonly considered pets, livestock,or commercially relevant animal species. The compositions andformulations may include partially or significantly purifiedpolypeptide, polynucleotide, or antibody or antigen binding fragmentcompositions, either alone, or in combination with one or moreadditional active ingredients, anticancer agents, vaccines, adjuvants,or other therapeutics which may be obtained from natural or recombinantsources, or which may be obtainable naturally or either chemicallysynthesized, or alternatively produced in vitro from recombinant hostcells expressing one or more nucleic acid segments that encode one ormore such additional active ingredients, carriers, adjuvants, cofactors,or other therapeutic compound.

[0201] 4.8 Diagnostic Reagents and Kits

[0202] The invention further provides diagnostic reagents and kitscomprising one or more such reagents for use in a variety of diagnosticassays, including for example, immunoassays such as ELISA and“sandwich”-type immunoassays. Such kits may preferably include at leasta first peptide, or a first antibody or antigen binding fragment of theinvention, a functional fragment thereof, or a cocktail thereof, andmeans for signal generation. The kit's components may be pre-attached toa solid support, or may be applied to the surface of a solid supportwhen the kit is used. The signal generating means may comepre-associated with an antibody of the invention or may requirecombination with one or more components, e.g., buffers, antibody-enzymeconjugates, enzyme substrates, or the like, prior to use. Kits may alsoinclude additional reagents, e.g., blocking reagents for reducingnonspecific binding to the solid phase surface, washing reagents, enzymesubstrates, and the like. The solid phase surface may be in the form ofmicrotiter plates, microspheres, or other materials suitable forimmobilizing proteins, peptides, or polypeptides. Preferably, an enzymethat catalyzes the formation of a chemiluminescent or chromogenicproduct or the reduction of a chemiluminescent or chromogenic substrateis a component of the signal generating means. Such enzymes are wellknown in the art.

[0203] Such kits are useful in the detection, monitoring and diagnosisof conditions characterized by over-expression or inappropriateexpression of hematological malignancy-related peptides, polypeptides,antibodies, and/or polynucleotides, as well as hybridomas, host cells,and vectors comprising one or more such compositions as disclosedherein.

[0204] The therapeutic and diagnostic kits of the present invention mayalso be prepared that comprise at least one of the antibody, peptide,antigen binding fragment, hybridoma, vector, vaccine, polynucleotide, orcellular compositions disclosed herein and instructions for using thecomposition as a diagnostic reagent or therapeutic agent. Containers foruse in such kits may typically comprise at least one vial, test tube,flask, bottle, syringe or other suitable container, into which one ormore of the diagnostic and/or therapeutic composition(s) may be placed,and preferably suitably aliquoted. Where a second therapeutic agent isalso provided, the kit may also contain a second distinct container intowhich this second diagnostic and/or therapeutic composition may beplaced. Alternatively, a plurality of compounds may be prepared in asingle pharmaceutical composition, and may be packaged in a singlecontainer means, such as a vial, flask, syringe, bottle, or othersuitable single container. The kits of the present invention will alsotypically include a means for containing the vial(s) in closeconfinement for commercial sale, such as, e.g., injection or blow-moldedplastic containers into which the desired vial(s) are retained. Where aradiolabel, chromogenic, fluorigenic, or other type of detectable labelor detecting means is included within the kit, the labeling agent may beprovided either in the same container as the diagnostic or therapeuticcomposition itself, or may alternatively be placed in a second distinctcontainer means into which this second composition may be placed andsuitably aliquoted. Alternatively, the detection reagent and the labelmay be prepared in a single container means, and in most cases, the kitwill also typically include a means for containing the vial(s) in closeconfinement for commercial sale and/or convenient packaging anddelivery.

[0205] 4.9 Polynucleotide Compositions

[0206] As used herein, the terms “DNA segment” and “polynucleotide”refer to a DNA molecule that has been isolated free of total genomic DNAof a particular species. Therefore, a DNA segment encoding a polypeptiderefers to a DNA segment that contains one or more coding sequences yetis substantially isolated away from, or purified free from, totalgenomic DNA of the species from which the DNA segment is obtained.Included within the terms “DNA segment” and “polynucleotide” are DNAsegments and smaller fragments of such segments, and also recombinantvectors, including, for example, plasmids, cosmids, phagemids, phage,viruses, and the like.

[0207] As will be understood by those skilled in the art, the DNAsegments of this invention can include genomic sequences, extra-genomicand plasmid-encoded sequences and smaller engineered gene segments thatexpress, or may be adapted to express, proteins, polypeptides, peptidesand the like. Such segments may be naturally isolated, or modifiedsynthetically by the hand of man.

[0208] “Isolated,” as used herein, means that a polynucleotide issubstantially away from other coding sequences, and that the DNA segmentdoes not contain large portions of unrelated coding DNA, such as largechromosomal fragments or other functional genes or polypeptide codingregions. Of course, this refers to the DNA segment as originallyisolated, and does not exclude genes or coding regions later added tothe segment by the hand of man.

[0209] As will be recognized by the skilled artisan, polynucleotides maybe single-stranded (coding or antisense) or double-stranded, and may beDNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules includeHnRNA molecules, which contain introns and correspond to a DNA moleculein a one-to-one manner, and mRNA molecules, which do not containintrons. Additional coding or non-coding sequences may, but need not, bepresent within a polynucleotide of the present invention, and apolynucleotide may, but need not, be linked to other molecules and/orsupport materials.

[0210] Polynucleotides may comprise a native sequence (i.e., anendogenous sequence that encodes a hematological malignancy-relatedtumor protein or a portion thereof) or may comprise a variant, or abiological or antigenic functional equivalent of such a sequence.Polynucleotide variants may contain one or more substitutions,additions, deletions and/or insertions, as further described below,preferably such that the immunogenicity of the encoded polypeptide isnot diminished, relative to a native tumor protein. The effect on theimmunogenicity of the encoded polypeptide may generally be assessed asdescribed herein. The term “variants” also encompasses homologous genesof xenogenic origin.

[0211] When comparing polynucleotide or polypeptide sequences, twosequences are said to be “identical” if the sequence of nucleotides oramino acids in the two sequences is the same when aligned for maximumcorrespondence, as described below. Comparisons between two sequencesare typically performed by comparing the sequences over a comparisonwindow to identify and compare local regions of sequence similarity. A“comparison window” as used herein, refers to a segment of at leastabout 20 contiguous positions, usually 30 to about 75, 40 to about 50,in which a sequence may be compared to a reference sequence of the samenumber of contiguous positions after the two sequences are optimallyaligned.

[0212] Optimal alignment of sequences for comparison may be conductedusing the Megalign program in the Lasergene suite of bioinformaticssoftware (DNASTAR, Inc., Madison, Wis.), using default parameters. Thisprogram embodies several alignment schemes described in the followingreferences: Dayhoff, M. O. (1978) A model of evolutionary change inproteins—Matrices for detecting distant relationships. In Dayhoff, M. O.(ed.) Atlas of Protein Sequence and Structure, National BiomedicalResearch Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; HeinJ. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.;Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E. W.and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971) Comb. Theor11:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P.H. A. and Sokal, R. R. (1973) Numerical Taxonomy—the Principles andPractice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.;Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA80:726-730.

[0213] Alternatively, optimal alignment of sequences for comparison maybe conducted by the local identity algorithm of Smith and Waterman(1981) Add. APL. Math 2:482, by the identity alignment algorithm ofNeedleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search forsimilarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci.USA 85: 2444, by computerized implementations of these algorithms (GAP,BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics SoftwarePackage, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.),or by inspection.

[0214] One preferred example of algorithms that are suitable fordetermining percent sequence identity and sequence similarity are theBLAST and BLAST 2.0 algorithms, which are described in Altschul et al.(1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol.Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used, forexample with the parameters described herein, to determine percentsequence identity for the polynucleotides and polypeptides of theinvention. Software for performing BLAST analyses is publicly availablethrough the National Center for Biotechnology Information. In oneillustrative example, cumulative scores can be calculated using, fornucleotide sequences, the parameters M (reward score for a pair ofmatching residues; always >0) and N (penalty score for mismatchingresidues; always <0). For amino acid sequences, a scoring matrix can beused to calculate the cumulative score. Extension of the word hits ineach direction are halted when: the cumulative alignment score falls offby the quantity X from its maximum achieved value; the cumulative scoregoes to zero or below, due to the accumulation of one or morenegative-scoring residue alignments; or the end of either sequence isreached. The BLAST algorithm parameters W, T and X determine thesensitivity and speed of the alignment. The BLASTN program (fornucleotide sequences) uses as defaults a wordlength (W) of 11, andexpectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff andHenikoff(1989) Proc. Natl. Acad. Sci. USA 89:10915) alignments, (B) of50, expectation (E) of 10, M=5, N=−4 and a comparison of both strands.

[0215] Preferably, the “percentage of sequence identity” is determinedby comparing two optimally aligned sequences over a window of comparisonof at least 20 positions, wherein the portion of the polynucleotide orpolypeptide sequence in the comparison window may comprise additions ordeletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent,or 10 to 12 percent, as compared to the reference sequences (which doesnot comprise additions or deletions) for optimal alignment of the twosequences. The percentage is calculated by determining the number ofpositions at which the identical nucleic acid bases or amino acidresidue occurs in both sequences to yield the number of matchedpositions, dividing the number of matched positions by the total numberof positions in the reference sequence (i.e., the window size) andmultiplying the results by 100 to yield the percentage of sequenceidentity.

[0216] Therefore, the present invention encompasses polynucleotide andpolypeptide sequences having substantial identity to the sequencesdisclosed herein, for example those comprising at least 50% sequenceidentity, preferably at least 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, or 99% or higher, sequence identity compared to apolynucleotide or polypeptide sequence of this invention using themethods described herein, (e.g., BLAST analysis using standardparameters, as described below). One skilled in this art will recognizethat these values can be appropriately adjusted to determinecorresponding identity of proteins encoded by two nucleotide sequencesby taking into account codon degeneracy, amino acid similarity, readingframe positioning and the like.

[0217] In additional embodiments, the present invention providesisolated polynucleotides and polypeptides comprising various lengths ofcontiguous stretches of sequence identical to or complementary to one ormore of the sequences disclosed herein. For example, polynucleotides areprovided by this invention that comprise at least about 15, 20, 30, 40,50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguousnucleotides of one or more of the sequences disclosed herein as well asall intermediate lengths there between. It will be readily understoodthat “intermediate lengths”, in this context, means any length betweenthe quoted values, such as 16, 17, 18, 19, etc.; 21, 22, 23, etc.; 30,31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151,152, 153, etc.; including all integers through 200-500; 500-1,000, andthe like.

[0218] The polynucleotides of the present invention, or fragmentsthereof, regardless of the length of the coding sequence itself, may becombined with other DNA sequences, such as promoters, polyadenylationsignals, additional restriction enzyme sites, multiple cloning sites,other coding segments, and the like, such that their overall length mayvary considerably. It is therefore contemplated that a nucleic acidfragment of almost any length may be employed, with the total lengthpreferably being limited by the ease of preparation and use in theintended recombinant DNA protocol. For example, illustrative DNAsegments with total lengths of about 10,000, about 5000, about 3000,about 2,000, about 1,000, about 500, about 200, about 100, about 50 basepairs in length, and the like, (including all intermediate lengths) arecontemplated to be useful in many implementations of this invention.

[0219] In other embodiments, the present invention is directed topolynucleotides that are capable of hybridizing under moderatelystringent conditions to a polynucleotide sequence provided herein, or afragment thereof, or a complementary sequence thereof. Hybridizationtechniques are well known in the art of molecular biology. For purposesof illustration, suitable moderately stringent conditions for testingthe hybridization of a polynucleotide of this invention with otherpolynucleotides include prewashing in a solution of 5×SSC, 0.5% SDS, 1.0mM EDTA (pH 8.0); hybridizing at 50° C.-65° C., 5×SSC, overnight;followed by washing twice at 65° C. for 20 minutes with each of 2×, 0.5×and 0.2×SSC containing 0.1% SDS.

[0220] Moreover, it will be appreciated by those of ordinary skill inthe art that, as a result of the degeneracy of the genetic code, thereare many nucleotide sequences that encode a polypeptide as describedherein. Some of these polynucleotides bear minimal homology to thenucleotide sequence of any native gene. Nonetheless, polynucleotidesthat vary due to differences in codon usage are specificallycontemplated by the present invention. Further, alleles of the genescomprising the polynucleotide sequences provided herein are within thescope of the present invention. Alleles are endogenous genes that arealtered as a result of one or more mutations, such as deletions,additions and/or substitutions of nucleotides. The resulting mRNA andprotein may, but need not, have an altered structure or function.Alleles may be identified using standard techniques (such ashybridization, amplification and/or database sequence comparison).

[0221] 4.10 Probes and Primers

[0222] In other embodiments of the present invention, the polynucleotidesequences provided herein can be advantageously used as probes orprimers for nucleic acid hybridization. As such, it is contemplated thatnucleic acid segments that comprise a sequence region of at least about15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95nucleotide long contiguous sequence that has the same sequence as, or iscomplementary to, at least a 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65,70, 75, 80, 85, 90, or 95 nucleotide long contiguous sequence asdisclosed in any one of SEQ ID NO:9598 to n SEQ ID NO:9610 will findparticular utility in a variety of hybridization embodiments. Longercontiguous identical or complementary sequences, e.g., those of about100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230,240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370,380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 525,550, 575, 600, 650, 700, 750, 800, 850, 900, 950, or even 1000 or sonucleotides (including all intermediate lengths) and all full-lengthsequences as disclosed in SEQ ID NO:9598 to SEQ ID NO:9610 will also beof use in certain embodiments as probes, primers, or amplificationtargets and such like.

[0223] The ability of such nucleic acid probes to specifically hybridizeto a sequence of interest will enable them to be of use in detecting thepresence of complementary sequences in a given sample. However, otheruses are also envisioned, such as the use of the sequence informationfor the preparation of mutant species primers, or primers, for use inpreparing other genetic constructions, and for identifying andcharacterizing full-length polynucleotides and full, or substantiallyfull-length cDNAs, mRNAs, and such like.

[0224] Polynucleotide molecules having sequence regions consisting ofcontiguous nucleotide stretches identical or complementary to one ormore polynucleotide sequences as disclosed herein, are particularlycontemplated as hybridization probes for use in, e.g., Southernhybridization analyses and Northern blotting. This would allow a geneproduct, or fragment thereof, to be analyzed, both in diverse cell typesand also in various bacterial cells. The total size of fragment, as wellas the size of the complementary stretch(es), will ultimately depend onthe intended use or application of the particular nucleic acid segment.Smaller fragments will generally find use in hybridization embodiments,wherein the length of the contiguous complementary region may be varied,such as between about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60 or so andup to and including larger contiguous complementary sequences, includingthose of about 70, 80, 90, 100, 120, 140, 160, 180, or 200 or sonucleotides in length may also be used, according to the given desiredgoal, and the particular length of the complementary sequences onewishes to detect by hybridization analysis.

[0225] The use of a hybridization probe of about between about 20 andabout 500 nucleotides in length allows the formation of a duplexmolecule that is both stable and selective. Molecules having contiguouscomplementary sequences over stretches greater than about 20 or so basesin length are generally preferred, though, in order to increasestability and selectivity of the hybrid, and thereby improve the qualityand degree of specific hybrid molecules obtained. One will generallyprefer to design nucleic acid molecules having gene-complementarystretches of between about 25 and 300 or so contiguous nucleotides, oreven longer where desired.

[0226] Hybridization probes may be selected from any portion of any ofthe sequences disclosed herein. All that is required is to review thesequence set forth in any one of SEQ ID NO:9598 through SEQ ID NO:9610,or to any contiguous portion of such a sequence, from about 15 to 30nucleotides in length up to and including the full length sequencesdisclosed in any one of SEQ ID NO:9598 through SEQ ID NO:9610, that onewishes to utilize as a probe or primer. The choice of probe and primersequences may be governed by various factors. For example, one may wishto employ primers from towards the termini of the total sequence.

[0227] Small polynucleotide segments or fragments may be readilyprepared by, for example, directly synthesizing the fragment by chemicalmeans, as is commonly practiced using an automated oligonucleotidesynthesizer. Also, fragments may be obtained by application of nucleicacid reproduction technology, such as the PCR™ technology of U.S. Pat.No. 4,683,202 (incorporated herein by reference), by introducingselected sequences into recombinant vectors for recombinant production,and by other recombinant DNA techniques generally known to those ofskill in the art of molecular biology.

[0228] The nucleotide sequences of the invention may be used for theirability to selectively form duplex molecules with complementarystretches of the entire gene or gene fragments of interest. Depending onthe application envisioned, one will typically desire to employ varyingconditions of hybridization to achieve varying degrees of selectivity ofprobe towards target sequence. For applications requiring highselectivity, one will typically desire to employ relatively stringentconditions to form the hybrids, e.g., one will select relatively lowsalt and/or high temperature conditions, such as provided by a saltconcentration of from about 0.02 M to about 0.15 M salt at temperaturesof from about 50° C. to about 70° C. Such selective conditions toleratelittle, if any, mismatch between the probe and the template or targetstrand, and would be particularly suitable for isolating relatedsequences.

[0229] Of course, for some applications, for example, where one desiresto prepare mutants employing a mutant primer strand hybridized to anunderlying template, less stringent (reduced stringency) hybridizationconditions will typically be needed in order to allow formation of theheteroduplex. In these circumstances, one may desire to employ saltconditions such as those of from about 0.15 M to about 0.9 M salt, attemperatures ranging from about 20° C. to about 55° C. Cross-hybridizingspecies can thereby be readily identified as positively hybridizingsignals with respect to control hybridizations. In any case, it isgenerally appreciated that conditions can be rendered more stringent bythe addition of increasing amounts of formamide, which serves todestabilize the hybrid duplex in the same manner as increasedtemperature. Thus, hybridization conditions can be readily manipulated,and thus will generally be a method of choice depending on the desiredresults.

[0230] 4.11 Polynucleotide Identification and Characterization

[0231] Polynucleotides may be identified, prepared and/or manipulatedusing any of a variety of well established techniques. For example, apolynucleotide may be identified, as described in more detail below, byscreening a microarray of cDNAs for tumor-associated expression (i.e.,expression that is at least two fold greater in a tumor than in normaltissue, as determined using a representative assay provided herein).Such screens may be performed, for example, using a Synteni microarray(Palo Alto, Calif.) according to the manufacturer's instructions (andessentially as described by Schena et al., Proc. Natl. Acad. Sci. USA93:10614-10619, 1996 and Heller et al., Proc. Natl. Acad. Sci. USA94:2150-2155, 1997). Alternatively, polynucleotides may be amplifiedfrom cDNA prepared from cells expressing the proteins described herein,such as hematological malignancy-related tumor cells. Suchpolynucleotides may be amplified via polymerase chain reaction (PCR).For this approach, sequence-specific primers may be designed based onthe sequences provided herein, and may be purchased or synthesized.

[0232] An amplified portion of a polynucleotide of the present inventionmay be used to isolate a full length gene from a suitable library (e.g.,a hematological malignancy-related tumor cDNA library) using well knowntechniques. Within such techniques, a library (cDNA or genomic) isscreened using one or more polynucleotide probes or primers suitable foramplification. Preferably, a library is size-selected to include largermolecules. Random primed libraries may also be preferred for identifying5′ and upstream regions of genes. Genomic libraries are preferred forobtaining introns and extending 5′ sequences.

[0233] For hybridization techniques, a partial sequence may be labeled(e.g., by nick-translation or end-labeling with ³²P) using well knowntechniques. A bacterial or bacteriophage library is then generallyscreened by hybridizing filters containing denatured bacterial colonies(or lawns containing phage plaques) with the labeled probe (see Sambrooket al., Molecular Cloning: A Laboratory Manual, Cold Spring HarborLaboratories, Cold Spring Harbor, N.Y., 1989). Hybridizing colonies orplaques are selected and expanded, and the DNA is isolated for furtheranalysis. cDNA clones may be analyzed to determine the amount ofadditional sequence by, for example, PCR using a primer from the partialsequence and a primer from the vector. Restriction maps and partialsequences may be generated to identify one or more overlapping clones.The complete sequence may then be determined using standard techniques,which may involve generating a series of deletion clones. The resultingoverlapping sequences can then assembled into a single contiguoussequence. A full length cDNA molecule can be generated by ligatingsuitable fragments, using well known techniques.

[0234] Alternatively, there are numerous amplification techniques forobtaining a full length coding sequence from a partial cDNA sequence.Within such techniques, amplification is generally performed via PCR.Any of a variety of commercially available kits may be used to performthe amplification step. Primers may be designed using, for example,software or algorithms or formulas well known in the art.

[0235] One such amplification technique is inverse PCR (see Triglia etal., Nucl. Acids Res. 16:8186, 1988), which uses restriction enzymes togenerate a fragment in the known region of the gene. The fragment isthen circularized by intramolecular ligation and used as a template forPCR with divergent primers derived from the known region. Within analternative approach, sequences adjacent to a partial sequence may beretrieved by amplification with a primer to a linker sequence and aprimer specific to a known region. The amplified sequences are typicallysubjected to a second round of amplification with the same linker primerand a second primer specific to the known region. A variation on thisprocedure, which employs two primers that initiate extension in oppositedirections from the known sequence, is described in WO 96/38591. Anothersuch technique is known as “rapid amplification of cDNA ends” or RACE.This technique involves the use of an internal primer and an externalprimer, which hybridizes to a polyA region or vector sequence, toidentify sequences that are 5′ and 3′ of a known sequence. Additionaltechniques include capture PCR (Lagerstrom et al., PCR Methods Applic.1:111-19, 1991) and walking PCR (Parker et al., Nucl. Acids. Res.19:3055-60, 1991). Other methods employing amplification may also beemployed to obtain a full length cDNA sequence.

[0236] In certain instances, it is possible to obtain a full length cDNAsequence by analysis of sequences provided in an expressed sequence tag(EST) database, such as that available from GenBank. Searches foroverlapping ESTs may generally be performed using well known programs(e.g., NCBI BLAST searches), and such ESTs may be used to generate acontiguous full length sequence. Full length DNA sequences may also beobtained by analysis of genomic fragments. 4.12 POLYNUCLEOTIDEEXPRESSION 1N HOST CELLS

[0237] In other embodiments of the invention, polynucleotide sequencesor fragments thereof which encode polypeptides of the invention, orfusion proteins or functional equivalents thereof, may be used inrecombinant DNA molecules to direct expression of a polypeptide inappropriate host cells. Due to the inherent degeneracy of the geneticcode, other DNA sequences that encode substantially the same or afunctionally equivalent amino acid sequence may be produced and thesesequences may be used to clone and express a given polypeptide.

[0238] As will be understood by those of skill in the art, it may beadvantageous in some instances to produce polypeptide-encodingnucleotide sequences possessing non-naturally occurring codons. Forexample, codons preferred by a particular prokaryotic or eukaryotic hostcan be selected to increase the rate of protein expression or to producea recombinant RNA transcript having desirable properties, such as ahalf-life which is longer than that of a transcript generated from thenaturally occurring sequence.

[0239] Moreover, the polynucleotide sequences of the present inventioncan be engineered using methods generally known in the art in order toalter polypeptide encoding sequences for a variety of reasons, includingbut not limited to, alterations which modify the cloning, processing,and/or expression of the gene product. For example, DNA shuffling byrandom fragmentation and PCR reassembly of gene fragments and syntheticoligonucleotides may be used to engineer the nucleotide sequences. Inaddition, site-directed mutagenesis may be used to insert newrestriction sites, alter glycosylation patterns, change codonpreference, produce splice variants, or introduce mutations, and soforth.

[0240] In another embodiment of the invention, natural, modified, orrecombinant nucleic acid sequences may be ligated to a heterologoussequence to encode a fusion protein. For example, to screen peptidelibraries for inhibitors of polypeptide activity, it may be useful toencode a chimeric protein that can be recognized by a commerciallyavailable antibody. A fusion protein may also be engineered to contain acleavage site located between the polypeptide-encoding sequence and theheterologous protein sequence, so that the polypeptide may be cleavedand purified away from the heterologous moiety.

[0241] Sequences encoding a desired polypeptide may be synthesized, inwhole or in part, using chemical methods well known in the art (seeCaruthers, M. H. et al. (1980) Nucl. Acids Res. Symp. Ser. 215-223,Horn, T. et al. (1980) Nucl. Acids Res. Symp. Ser. 225-232).Alternatively, the protein itself may be produced using chemical methodsto synthesize the amino acid sequence of a polypeptide, or a portionthereof. For example, peptide synthesis can be performed using varioussolid-phase techniques (Roberge, J. Y. et al. (1995) Science269:202-204) and automated synthesis may be achieved, for example, usingthe ABI 431A Peptide Synthesizer (Perkin Elmer, Palo Alto, Calif.).

[0242] A newly synthesized peptide may be substantially purified bypreparative high performance liquid chromatography (e.g., Creighton, T.(1983) Proteins, Structures and Molecular Principles, WH Freeman andCo., New York, N.Y.) or other comparable techniques available in theart. The composition of the synthetic peptides may be confirmed by aminoacid analysis or sequencing (e.g., the Edman degradation procedure).Additionally, the amino acid sequence of a polypeptide, or any partthereof, may be altered during direct synthesis and/or combined usingchemical methods with sequences from other proteins, or any partthereof, to produce a variant polypeptide.

[0243] In order to express a desired polypeptide, the nucleotidesequences encoding the polypeptide, or functional equivalents, may beinserted into appropriate expression vector, i.e., a vector whichcontains the necessary elements for the transcription and translation ofthe inserted coding sequence. Methods which are well known to thoseskilled in the art may be used to construct expression vectorscontaining sequences encoding a polypeptide of interest and appropriatetranscriptional and translational control elements. These methodsinclude in vitro recombinant DNA techniques, synthetic techniques, andin vivo genetic recombination. Such techniques are described inSambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, ColdSpring Harbor Press, Plainview, N.Y., and Ausubel, F. M. et al. (1989)Current Protocols in Molecular Biology, John Wiley & Sons, New York.N.Y.

[0244] A variety of expression vector/host systems may be utilized tocontain and express polynucleotide sequences. These include, but are notlimited to, microorganisms such as bacteria transformed with recombinantbacteriophage, plasmid, or cosmid DNA expression vectors; yeasttransformed with yeast expression vectors; insect cell systems infectedwith virus expression vectors (e.g., baculovirus); plant cell systemstransformed with virus expression vectors (e.g., cauliflower mosaicvirus, CaMV; tobacco mosaic virus, TMV) or with bacterial expressionvectors (e.g., Ti or pBR322 plasmids); or animal cell systems.

[0245] The “control elements” or “regulatory sequences” present in anexpression vector are those non-translated regions of thevector—enhancers, promoters, 5′ and 3′ untranslated regions—whichinteract with host cellular proteins to carry out transcription andtranslation. Such elements may vary in their strength and specificity.Depending on the vector system and host utilized, any number of suitabletranscription and translation elements, including constitutive andinducible promoters, may be used. For example, when cloning in bacterialsystems, inducible promoters such as the hybrid lacZ promoter of thePBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid(Gibco BRL, Gaithersburg, Md.) and the like may be used. In mammaliancell systems, promoters from mammalian genes or from mammalian virusesare generally preferred. If it is necessary to generate a cell line thatcontains multiple copies of the sequence encoding a polypeptide, vectorsbased on SV40 or EBV may be advantageously used with an appropriateselectable marker.

[0246] In bacterial systems, a number of expression vectors may beselected depending upon the use intended for the expressed polypeptide.For example, when large quantities are needed, for example for theinduction of antibodies, vectors which direct high level expression offusion proteins that are readily purified may be used. Such vectorsinclude, but are not limited to, the multifunctional E. coli cloning andexpression vectors such as BLUESCRIPT (Stratagene), in which thesequence encoding the polypeptide of interest may be ligated into thevector in frame with sequences for the amino-terminal Met and thesubsequent 7 residues of .beta.-galactosidase so that a hybrid proteinis produced; pIN vectors (Van Heeke, G. and S. M. Schuster (1989) J.Biol. Chem. 264:5503-5509); and the like. pGEX Vectors (Promega,Madison, Wis.) may also be used to express foreign polypeptides asfusion proteins with glutathione S-transferase (GST). In general, suchfusion proteins are soluble and can easily be purified from lysed cellsby adsorption to glutathione-agarose beads followed by elution in thepresence of free glutathione. Proteins made in such systems may bedesigned to include heparin, thrombin, or factor XA protease cleavagesites so that the cloned polypeptide of interest can be released fromthe GST moiety at will.

[0247] In the yeast, Saccharomyces cerevisiae, a number of vectorscontaining constitutive or inducible promoters such as alpha factor,alcohol oxidase, and PGH may be used. For reviews, see Ausubel et al.(supra) and Grant et al. (1987) Methods Enzymol. 153:516-544.

[0248] In cases where plant expression vectors are used, the expressionof sequences encoding polypeptides may be driven by any of a number ofpromoters. For example, viral promoters such as the 35S and 19Spromoters of CaMV may be used alone or in combination with the omegaleader sequence from TMV (Takamatsu, N. (1987) EMBO J. 6:307-311.Alternatively, plant promoters such as the small subunit of RUBISCO orheat shock promoters may be used (Coruzzi, G. et al. (1984) EMBO J.3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter,J. et al. (1991) Results Probl. Cell Differ. 17:85-105). Theseconstructs can be introduced into plant cells by direct DNAtransformation or pathogen-mediated transfection. Such techniques aredescribed in a number of generally available reviews (see, for example,Hobbs, S. or Murry, L. E. in McGraw Hill Yearbook of Science andTechnology (1992) McGraw Hill, New York, N.Y.; pp. 191-196).

[0249] An insect system may also be used to express a polypeptide ofinterest. For example, in one such system, Autographa californicanuclear polyhedrosis virus (AcNPV) is used as a vector to expressforeign genes in Spodoptera frugiperda cells or in Trichoplusia larvae.The sequences encoding the polypeptide may be cloned into anon-essential region of the virus, such as the polyhedrin gene, andplaced under control of the polyhedrin promoter. Successful insertion ofthe polypeptide-encoding sequence will render the polyhedrin geneinactive and produce recombinant virus lacking coat protein. Therecombinant viruses may then be used to infect, for example, S.frugiperda cells or Trichoplusia larvae in which the polypeptide ofinterest may be expressed (Engelhard, E. K. et al. (1994) Proc. Natl.Acad. Sci. 91 :3224-3227).

[0250] In mammalian host cells, a number of viral-based expressionsystems are generally available. For example, in cases where anadenovirus is used as an expression vector, sequences encoding apolypeptide of interest may be ligated into an adenovirustranscription/translation complex consisting of the late promoter andtripartite leader sequence. Insertion in a non-essential E1 or E3 regionof the viral genome may be used to obtain a viable virus which iscapable of expressing the polypeptide in infected host cells (Logan, J.and Shenk, T. (1984) Proc. Natl. Acad. Sci. 81:3655-3659). In addition,transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer,may be used to increase expression in mammalian host cells.

[0251] Specific initiation signals may also be used to achieve moreefficient translation of sequences encoding a polypeptide of interest.Such signals include the ATG initiation codon and adjacent sequences. Incases where sequences encoding the polypeptide, its initiation codon,and upstream sequences are inserted into the appropriate expressionvector, no additional transcriptional or translational control signalsmay be needed. However, in cases where only coding sequence, or aportion thereof, is inserted, exogenous translational control signalsincluding the ATG initiation codon should be provided. Furthermore, theinitiation codon should be in the correct reading frame to ensuretranslation of the entire insert. Exogenous translational elements andinitiation codons may be of various origins, both natural and synthetic.The efficiency of expression may be enhanced by the inclusion ofenhancers which are appropriate for the particular cell system which isused, such as those described in the literature (Scharf, D. et al.(1994) Results Probl. Cell Differ. 20:125-162).

[0252] In addition, a host cell strain may be chosen for its ability tomodulate the expression of the inserted sequences or to process theexpressed protein in the desired fashion. Such modifications of thepolypeptide include, but are not limited to, acetylation, carboxylation.glycosylation, phosphorylation, lipidation, and acylation.Post-translational processing which cleaves a “prepro” form of theprotein may also be used to facilitate correct insertion, folding and/orfunction. Different host cells such as CHO, HeLa, MDCK, HEK293, andW138, which have specific cellular machinery and characteristicmechanisms for such post-translational activities, may be chosen toensure the correct modification and processing of the foreign protein.

[0253] For long-term, high-yield production of recombinant proteins,stable expression is generally preferred. For example, cell lines whichstably express a polynucleotide of interest may be transformed usingexpression vectors which may contain viral origins of replication and/orendogenous expression elements and a selectable marker gene on the sameor on a separate vector. Following the introduction of the vector, cellsmay be allowed to grow for 1-2 days in an enriched media before they areswitched to selective media. The purpose of the selectable marker is toconfer resistance to selection, and its presence allows growth andrecovery of cells which successfully express the introduced sequences.Resistant clones of stably transformed cells may be proliferated usingtissue culture techniques appropriate to the cell type.

[0254] Any number of selection systems may be used to recovertransformed cell lines. These include, but are not limited to, theherpes simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell11:223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1990)Cell 22:817-23) genes which can be employed in tk.sup.- or aprt.sup.-cells, respectively. Also, antimetabolite, antibiotic or herbicideresistance can be used as the basis for selection; for example, dhfrwhich confers resistance to methotrexate (Wigler, M. et al. (1980) Proc.Natl. Acad. Sci. 77:3567-70); npt, which confers resistance to theaminoglycosides, neomycin and G-418 (Colbere-Garapin, F. et al (1981) J.Mol. Biol. 150:1-14); and als or pat, which confer resistance tochlorsulfuron and phosphinotricin acetyltransferase, respectively(Murry, supra). Additional selectable genes have been described, forexample, trpB, which allows cells to utilize indole in place oftryptophan, or hisD, which allows cells to utilize histinol in place ofhistidine (Hartman, S.C. and R. C. Mulligan (1988) Proc. Natl. Acad.Sci. 85:8047-51). Recently, the use of visible markers has gainedpopularity with such markers as anthocyanins, beta-glucuronidase and itssubstrate GUS, and luciferase and its substrate luciferin, being widelyused not only to identify transformants, but also to quantify the amountof transient or stable protein expression attributable to a specificvector system (Rhodes, C. A. et al. (1995) Methods Mol. Biol.55:121-131).

[0255] Although the presence/absence of marker gene expression suggeststhat the gene of interest is also present, its presence and expressionmay need to be confirmed. For example, if the sequence encoding apolypeptide is inserted within a marker gene sequence, recombinant cellscontaining sequences can be identified by the absence of marker genefunction. Alternatively, a marker gene can be placed in tandem with apolypeptide-encoding sequence under the control of a single promoter.Expression of the marker gene in response to induction or selectionusually indicates expression of the tandem gene as well.

[0256] Alternatively, host cells which contain and express a desiredpolynucleotide sequence may be identified by a variety of proceduresknown to those of skill in the art. These procedures include, but arenot limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassayor immunoassay techniques which include membrane, solution, or chipbased technologies for the detection and/or quantification of nucleicacid or protein.

[0257] A variety of protocols for detecting and measuring the expressionof polynucleotide-encoded products, using either polyclonal ormonoclonal antibodies specific for the product are known in the art.Examples include enzyme-linked immunosorbent assay (ELISA),radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS).A two-site, monoclonal-based immunoassay utilizing monoclonal antibodiesreactive to two non-interfering epitopes on a given polypeptide may bepreferred for some applications, but a competitive binding assay mayalso be employed. These and other assays are described, among otherplaces, in Hampton, R. et al. (1990; Serological Methods, a LaboratoryManual, APS Press, St Paul. Minn.) and Maddox, D. E. et al. (1983; J.Exp. Med. 158:1211-1216).

[0258] A wide variety of labels and conjugation techniques are known bythose skilled in the art and may be used in various nucleic acid andamino acid assays. Means for producing labeled hybridization or PCRprobes for detecting sequences related to polynucleotides includeoligolabeling, nick translation, end-labeling or PCR amplification usinga labeled nucleotide. Alternatively, the sequences, or any portionsthereof may be cloned into a vector for the production of an mRNA probe.Such vectors are known in the art, are commercially available, and maybe used to synthesize RNA probes in vitro by addition of an appropriateRNA polymerase such as T7, T3, or SP6 and labeled nucleotides. Theseprocedures may be conducted using a variety of commercially availablekits. Suitable reporter molecules or labels, which may be used includeradionuclides, enzymes, fluorescent, chemiluminescent, or chromogenicagents as well as substrates, cofactors, inhibitors, magnetic particles,and the like.

[0259] Host cells transformed with a polynucleotide sequence of interestmay be cultured under conditions suitable for the expression andrecovery of the protein from cell culture. The protein produced by arecombinant cell may be secreted or contained intracellularly dependingon the sequence and/or the vector used. As will be understood by thoseof skill in the art, expression vectors containing polynucleotides ofthe invention may be designed to contain signal sequences which directsecretion of the encoded polypeptide through a prokaryotic or eukaryoticcell membrane. Other recombinant constructions may be used to joinsequences encoding a polypeptide of interest to nucleotide sequenceencoding a polypeptide domain which will facilitate purification ofsoluble proteins. Such purification facilitating domains include, butare not limited to, metal chelating peptides such ashistidine-tryptophan modules that allow purification on immobilizedmetals, protein A domains that allow purification on immobilizedimmunoglobulin, and the domain utilized in the FLAGS extension/affinitypurification system (Immunex Corp., Seattle, Wash.). The inclusion ofcleavable linker sequences such as those specific for Factor XA orenterokinase (Invitrogen. San Diego, Calif.) between the purificationdomain and the encoded polypeptide may be used to facilitatepurification. One such expression vector provides for expression of afusion protein containing a polypeptide of interest and a nucleic acidencoding 6 histidine residues preceding a thioredoxin or an enterokinasecleavage site. The histidine residues facilitate purification on IMIAC(immobilized metal ion affinity chromatography) as described in Porath,J. et al. (1992, Prot. Exp. Purif. 3:263-281) while the enterokinasecleavage site provides a means for purifying the desired polypeptidefrom the fusion protein. A discussion of vectors which contain fusionproteins is provided in Kroll, D. J. et al. (1993; DNA Cell Biol.12:441-453).

[0260] In addition to recombinant production methods, polypeptides ofthe invention, and fragments thereof, may be produced by direct peptidesynthesis using solid-phase techniques (Merrifield J. (1963) J. Am.Chem. Soc. 85:2149-2154). Protein synthesis may be performed usingmanual techniques or by automation. Automated synthesis may be achieved,for example, using Applied Biosystems 431A Peptide Synthesizer (PerkinElmer). Alternatively, various fragments may be chemically synthesizedseparately and combined using chemical methods to produce the fulllength molecule.

[0261] 4.13 Site-Specific Mutagenesis

[0262] Site-specific mutagenesis is a technique useful in thepreparation of individual peptides, or biologically functionalequivalent polypeptides, through specific mutagenesis of the underlyingpolynucleotides that encode them. The technique, well-known to those ofskill in the art, further provides a ready ability to prepare and testsequence variants, for example, incorporating one or more of theforegoing considerations, by introducing one or more nucleotide sequencechanges into the DNA. Site-specific mutagenesis allows the production ofmutants through the use of specific oligonucleotide sequences whichencode the DNA sequence of the desired mutation, as well as a sufficientnumber of adjacent nucleotides, to provide a primer sequence ofsufficient size and sequence complexity to form a stable duplex on bothsides of the deletion junction being traversed. Mutations may beemployed in a selected polynucleotide sequence to improve, alter,decrease, modify, or otherwise change the properties of thepolynucleotide itself, and/or alter the properties, activity,composition, stability, or primary sequence of the encoded polypeptide.

[0263] In certain embodiments of the present invention, the inventorscontemplate the mutagenesis of the disclosed polynucleotide sequences toalter one or more properties of the encoded polypeptide, such as theantigenicity of a polypeptide vaccine. The techniques of site-specificmutagenesis are well-known in the art, and are widely used to createvariants of both polypeptides and polynucleotides. For example,site-specific mutagenesis is often used to alter a specific portion of aDNA molecule. In such embodiments, a primer comprising typically about14 to about 25 nucleotides or so in length is employed, with about 5 toabout 10 residues on both sides of the junction of the sequence beingaltered.

[0264] As will be appreciated by those of skill in the art,site-specific mutagenesis techniques have often employed a phage vectorthat exists in both a single stranded and double stranded form. Typicalvectors useful in site-directed mutagenesis include vectors such as theM13 phage. These phage are readily commercially-available and their useis generally well-known to those skilled in the art. Double-strandedplasmids are also routinely employed in site directed mutagenesis thateliminates the step of transferring the gene of interest from a plasmidto a phage.

[0265] In general, site-directed mutagenesis in accordance herewith isperformed by first obtaining a single-stranded vector or melting apartof two strands of a double-stranded vector that includes within itssequence a DNA sequence that encodes the desired peptide. Anoligonucleotide primer bearing the desired mutated sequence is prepared,generally synthetically. This primer is then annealed with thesingle-stranded vector, and subjected to DNA polymerizing enzymes suchas E. coli polymerase I Klenow fragment, in order to complete thesynthesis of the mutation-bearing strand. Thus, a heteroduplex is formedwherein one strand encodes the original non-mutated sequence and thesecond strand bears the desired mutation. This heteroduplex vector isthen used to transform appropriate cells, such as E. coli cells, andclones are selected which include recombinant vectors bearing themutated sequence arrangement.

[0266] The preparation of sequence variants of the selectedpeptide-encoding DNA segments using site-directed mutagenesis provides ameans of producing potentially useful species and is not meant to belimiting as there are other ways in which sequence variants of peptidesand the DNA sequences encoding them may be obtained. For example,recombinant vectors encoding the desired peptide sequence may be treatedwith mutagenic agents, such as hydroxylamine, to obtain sequencevariants. Specific details regarding these methods and protocols arefound in the teachings of Maloy et al., 1994; Segal, 1976; Prokop andBajpai, 1991; Kuby, 1994; and Maniatis et al., 1982, each incorporatedherein by reference, for that purpose.

[0267] As used herein, the term “oligonucleotide directed mutagenesisprocedure” refers to template-dependent processes and vector-mediatedpropagation which result in an increase in the concentration of aspecific nucleic acid molecule relative to its initial concentration, orin an increase in the concentration of a detectable signal, such asamplification. As used herein, the term “oligonucleotide directedmutagenesis procedure” is intended to refer to a process that involvesthe template-dependent extension of a primer molecule. The term templatedependent process refers to nucleic acid synthesis of an RNA or a DNAmolecule wherein the sequence of the newly synthesized strand of nucleicacid is dictated by the well-known rules of complementary base pairing(see, for example, Watson, 1987). Typically, vector mediatedmethodologies involve the introduction of the nucleic acid fragment intoa DNA or RNA vector, the clonal amplification of the vector, and therecovery of the amplified nucleic acid fragment. Examples of suchmethodologies are provided by U.S. Pat. No. 4,237,224, specificallyincorporated herein by reference in its entirety.

[0268] 4.14 Polynucleotide Amplification Techniques

[0269] A number of template dependent processes are available to amplifythe target sequences of interest present in a sample. One of the bestknown amplification methods is the polymerase chain reaction (PCR™)which is described in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and4,800,159, each of which is incorporated herein by reference in itsentirety. Briefly, in PCR™, two primer sequences are prepared which arecomplementary to regions on opposite complementary strands of the targetsequence. An excess of deoxynucleoside triphosphates is added to areaction mixture along with a DNA polymerase (e.g., Taq polymerase). Ifthe target sequence is present in a sample, the primers will bind to thetarget and the polymerase will cause the primers to be extended alongthe target sequence by adding on nucleotides. By raising and loweringthe temperature of the reaction mixture, the extended primers willdissociate from the target to form reaction products, excess primerswill bind to the target and to the reaction product and the process isrepeated. Preferably reverse transcription and PCR™ amplificationprocedure may be performed in order to quantify the amount of mRNAamplified. Polymerase chain reaction methodologies are well known in theart.

[0270] Another method for amplification is the ligase chain reaction(referred to as LCR), disclosed in Eur. Pat. Appl. Publ. No. 320,308(specifically incorporated herein by reference in its entirety). In LCR,two complementary probe pairs are prepared, and in the presence of thetarget sequence, each pair will bind to opposite complementary strandsof the target such that they abut. In the presence of a ligase, the twoprobe pairs will link to form a single unit. By temperature cycling, asin PCR™, bound ligated units dissociate from the target and then serveas “target sequences” for ligation of excess probe pairs. U.S. Pat. No.4,883,750, incorporated herein by reference in its entirety, describesan alternative method of amplification similar to LCR for binding probepairs to a target sequence.

[0271] Qbeta Replicase, described in PCT Intl. Pat. Appl. Publ. No.PCT/US87/00880, incorporated herein by reference in its entirety, mayalso be used as still another amplification method in the presentinvention. In this method, a replicative sequence of RNA that has aregion complementary to that of a target is added to a sample in thepresence of an RNA polymerase. The polymerase will copy the replicativesequence that can then be detected.

[0272] An isothermal amplification method, in which restrictionendonucleases and ligases are used to achieve the amplification oftarget molecules that contain nucleotide 5′-[α-thio]triphosphates in onestrand of a restriction site (Walker et al., 1992, incorporated hereinby reference in its entirety), may also be useful in the amplificationof nucleic acids in the present invention.

[0273] Strand Displacement Amplification (SDA) is another method ofcarrying out isothermal amplification of nucleic acids which involvesmultiple rounds of strand displacement and synthesis, i.e. nicktranslation. A similar method, called Repair Chain Reaction (RCR) isanother method of amplification which may be useful in the presentinvention and is involves annealing several probes throughout a regiontargeted for amplification, followed by a repair reaction in which onlytwo of the four bases are present. The other two bases can be added asbiotinylated derivatives for easy detection. A similar approach is usedin SDA.

[0274] Sequences can also be detected using a cyclic probe reaction(CPR). In CPR, a probe having a 3′ and 5′ sequences of non-target DNAand an internal or “middle” sequence of the target protein specific RNAis hybridized to DNA which is present in a sample. Upon hybridization,the reaction is treated with RNaseH, and the products of the probe areidentified as distinctive products by generating a signal that isreleased after digestion. The original template is annealed to anothercycling probe and the reaction is repeated. Thus, CPR involvesamplifying a signal generated by hybridization of a probe to a targetgene specific expressed nucleic acid.

[0275] Still other amplification methods described in Great Britain Pat.Appl. No. 2 202 328, and in PCT Intl. Pat. Appl. Publ. No.PCT/US89/01025, each of which is incorporated herein by reference in itsentirety, may be used in accordance with the present invention. In theformer application, “modified” primers are used in a PCR-like, templateand enzyme dependent synthesis. The primers may be modified by labelingwith a capture moiety (e.g., biotin) and/or a detector moiety (e.g.,enzyme). In the latter application, an excess of labeled probes is addedto a sample. In the presence of the target sequence, the probe binds andis cleaved catalytically. After cleavage, the target sequence isreleased intact to be bound by excess probe. Cleavage of the labeledprobe signals the presence of the target sequence.

[0276] Other nucleic acid amplification procedures includetranscription-based amplification systems (TAS) (Kwoh et al., 1989; PCTIntl. Pat. Appl. Publ. No. WO 88/10315, incorporated herein by referencein its entirety), including nucleic acid sequence based amplification(NASBA) and 3SR. In NASBA, the nucleic acids can be prepared foramplification by standard phenol/chloroform extraction, heatdenaturation of a sample, treatment with lysis buffer and minispincolumns for isolation of DNA and RNA or guanidinium chloride extractionof RNA. These amplification techniques involve annealing a primer thathas sequences specific to the target sequence. Following polymerization,DNA/RNA hybrids are digested with RNase H while double stranded DNAmolecules are heat-denatured again. In either case the single strandedDNA is made fully double stranded by addition of second target-specificprimer, followed by polymerization. The double stranded DNA moleculesare then multiply transcribed by a polymerase such as T7 or SP6. In anisothermal cyclic reaction, the RNAs are reverse transcribed into DNA,and transcribed once again with a polymerase such as T7 or SP6. Theresulting products, whether truncated or complete, indicatetarget-specific sequences.

[0277] Eur. Pat. Appl. Publ. No. 329,822, incorporated herein byreference in its entirety, disclose a nucleic acid amplification processinvolving cyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA,and double-stranded DNA (dsDNA), which may be used in accordance withthe present invention. The ssRNA is a first template for a first primeroligonucleotide, which is elongated by reverse transcriptase(RNA-dependent DNA polymerase). The RNA is then removed from resultingDNA:RNA duplex by the action of ribonuclease H(RNase H, an RNasespecific for RNA in a duplex with either DNA or RNA). The resultantssDNA is a second template for a second primer, which also includes thesequences of an RNA polymerase promoter (exemplified by T7 RNApolymerase) 5′ to its homology to its template. This primer is thenextended by DNA polymerase (exemplified by the large “Klenow” fragmentof E. coli DNA polymerase I), resulting as a double-stranded DNA(“dsDNA”) molecule, having a sequence identical to that of the originalRNA between the primers and having additionally, at one end, a promotersequence. This promoter sequence can be used by the appropriate RNApolymerase to make many RNA copies of the DNA. These copies can thenre-enter the cycle leading to very swift amplification. With properchoice of enzymes, this amplification can be done isothermally withoutaddition of enzymes at each cycle. Because of the cyclical nature ofthis process, the starting sequence can be chosen to be in the form ofeither DNA or RNA.

[0278] PCT Intl. Pat. Appl. Publ. No. WO 89/06700, incorporated hereinby reference in its entirety, disclose a nucleic acid sequenceamplification scheme based on the hybridization of a promoter/primersequence to a target single-stranded DNA (“ssDNA”) followed bytranscription of many RNA copies of the sequence. This scheme is notcyclic; i.e. new templates are not produced from the resultant RNAtranscripts. Other amplification methods include “RACE” (Frohman, 1990),and “one-sided PCR” (Ohara, 1989) which are well-known to those of skillin the art.

[0279] Methods based on ligation of two (or more) oligonucleotides inthe presence of nucleic acid having the sequence of the resulting“di-oligonucleotide”, thereby amplifying the di-oligonucleotide (Wu andDean, 1996, incorporated herein by reference in its entirety), may alsobe used in the amplification of DNA sequences of the present invention.

[0280] 4.15 In Vivo Polynucleotide Delivery Techniques

[0281] In additional embodiments, genetic constructs comprising one ormore of the polynucleotides of the invention are introduced into cellsin vivo. This may be achieved using any of a variety or well knownapproaches, several of which are outlined below for the purpose ofillustration.

[0282] 4.15.1 Adenovirus

[0283] One of the preferred methods for in vivo delivery of one or morenucleic acid sequences involves the use of an adenovirus expressionvector. “Adenovirus expression vector” is meant to include thoseconstructs containing adenovirus sequences sufficient to (a) supportpackaging of the construct and (b) to express a polynucleotide that hasbeen cloned therein in a sense or antisense orientation. Of course, inthe context of an antisense construct, expression does not require thatthe gene product be synthesized.

[0284] The expression vector comprises a genetically engineered form ofan adenovirus. Knowledge of the genetic organization of adenovirus, a 36kb, linear, double-stranded DNA virus, allows substitution of largepieces of adenoviral DNA with foreign sequences up to 7 kb (Grunhaus andHorwitz, 1992). In contrast to retrovirus, the adenoviral infection ofhost cells does not result in chromosomal integration because adenoviralDNA can replicate in an episomal manner without potential genotoxicity.Also, adenoviruses are structurally stable, and no genome rearrangementhas been detected after extensive amplification. Adenovirus can infectvirtually all epithelial cells regardless of their cell cycle stage. Sofar, adenoviral infection appears to be linked only to mild disease suchas acute respiratory disease in humans.

[0285] Adenovirus is particularly suitable for use as a gene transfervector because of its mid-sized genome, ease of manipulation, hightiter, wide target-cell range and high infectivity. Both ends of theviral genome contain 100-200 base pair inverted repeats (ITRs), whichare cis elements necessary for viral DNA replication and packaging. Theearly (E) and late (L) regions of the genome contain differenttranscription units that are divided by the onset of viral DNAreplication. The E1 region (E1A and E1B) encodes proteins responsiblefor the regulation of transcription of the viral genome and a fewcellular genes. The expression of the E2 region (E2A and E2B) results inthe synthesis of the proteins for viral DNA replication. These proteinsare involved in DNA replication, late gene expression and host cellshut-off (Renan, 1990). The products of the late genes, including themajority of the viral capsid proteins, are expressed only aftersignificant processing of a single primary transcript issued by themajor late promoter (MLP). The MLP, (located at 16.8 m.u.) isparticularly efficient during the late phase of infection, and all themRNA's issued from this promoter possess a 5′-tripartite leader (TPL)sequence which makes them preferred mRNA's for translation.

[0286] In a current system, recombinant adenovirus is generated fromhomologous recombination between shuttle vector and provirus vector. Dueto the possible recombination between two proviral vectors, wild-typeadenovirus may be generated from this process. Therefore, it is criticalto isolate a single clone of virus from an individual plaque and examineits genomic structure.

[0287] Generation and propagation of the current adenovirus vectors,which are replication deficient, depend on a unique helper cell line,designated 293, which was transformed from human embryonic kidney cellsby AdS DNA fragments and constitutively expresses E1 proteins (Graham etal., 1977). Since the E3 region is dispensable from the adenovirusgenome (Jones and Shenk, 1978), the current adenovirus vectors, with thehelp of 293 cells, carry foreign DNA in either the E1, the D3 or bothregions (Graham and Prevec, 1991). In nature, adenovirus can packageapproximately 105% of the wild-type genome (Ghosh-Choudhury et al.,1987), providing capacity for about 2 extra kB of DNA. Combined with theapproximately 5.5 kB of DNA that is replaceable in the E1 and E3regions, the maximum capacity of the current adenovirus vector is under7.5 kB, or about 15% of the total length of the vector. More than 80% ofthe adenovirus viral genome remains in the vector backbone and is thesource of vector-borne cytotoxicity. Also, the replication deficiency ofthe E1-deleted virus is incomplete. For example, leakage of viral geneexpression has been observed with the currently available vectors athigh multiplicities of infection (MOD (Mulligan, 1993).

[0288] Helper cell lines may be derived from human cells such as humanembryonic kidney cells, muscle cells, hematopoietic cells or other humanembryonic mesenchymal or epithelial cells. Alternatively, the helpercells may be derived from the cells of other mammalian species that arepermissive for human adenovirus. Such cells include, e.g., Vero cells orother monkey embryonic mesenchymal or epithelial cells. As stated above,the currently preferred helper cell line is 293.

[0289] Recently, Racher et al. (1995) disclosed improved methods forculturing 293 cells and propagating adenovirus. In one format, naturalcell aggregates are grown by inoculating individual cells into 1 litersiliconized spinner flasks (Techne, Cambridge, UK) containing 100-200 mlof medium. Following stirring at 40 rpm, the cell viability is estimatedwith trypan blue. In another format, Fibra-Cel microcarriers (BibbySterlin, Stone, UK) (5 g/l) is employed as follows. A cell inoculum,resuspended in 5 ml of medium, is added to the carrier (50 ml) in a 250ml Erlenmeyer flask and left stationary, with occasional agitation, for1 to 4 h. The medium is then replaced with 50 ml of fresh medium andshaking initiated. For virus production, cells are allowed to grow toabout 80% confluence, after which time the medium is replaced (to 25% ofthe final volume) and adenovirus added at an MOI of 0.05. Cultures areleft stationary overnight, following which the volume is increased to100% and shaking commenced for another 72 h.

[0290] Other than the requirement that the adenovirus vector bereplication defective, or at least conditionally defective, the natureof the adenovirus vector is not believed to be crucial to the successfulpractice of the invention. The adenovirus may be of any of the 42different known serotypes or subgroups A-F. Adenovirus type 5 ofsubgroup C is the preferred starting material in order to obtain aconditional replication-defective adenovirus vector for use in thepresent invention, since Adenovirus type 5 is a human adenovirus aboutwhich a great deal of biochemical and genetic information is known, andit has historically been used for most constructions employingadenovirus as a vector.

[0291] As stated above, the typical vector according to the presentinvention is replication defective and will not have an adenovirus E1region. Thus, it will be most convenient to introduce the polynucleotideencoding the gene of interest at the position from which the E1-codingsequences have been removed. However, the position of insertion of theconstruct within the adenovirus sequences is not critical to theinvention. The polynucleotide encoding the gene of interest may also beinserted in lieu of the deleted E3 region in E3 replacement vectors asdescribed by Karlsson et al. (1986) or in the E4 region where a helpercell line or helper virus complements the E4 defect.

[0292] Adenovirus is easy to grow and manipulate and exhibits broad hostrange in vitro and in vivo. This group of viruses can be obtained inhigh titers, e.g., 10⁹-10¹¹ plaque-forming units per ml, and they arehighly infective. The life cycle of adenovirus does not requireintegration into the host cell genome. The foreign genes delivered byadenovirus vectors are episomal and, therefore, have low genotoxicity tohost cells. No side effects have been reported in studies of vaccinationwith wild-type adenovirus (Couch et al., 1963; Top et al., 1971),demonstrating their safety and therapeutic potential as in vivo genetransfer vectors.

[0293] Adenovirus vectors have been used in eukaryotic gene expression(Levrero et al., 1991; Gomez-Foix et al., 1992) and vaccine development(Grunhaus and Horwitz, 1992; Graham and Prevec, 1992). Recently, animalstudies suggested that recombinant adenovirus could be used for genetherapy (Stratford-Perricaudet and Perricaudet, 1991;Stratford-Perricaudet et al., 1990; Rich et al., 1993). Studies inadministering recombinant adenovirus to different tissues includetrachea instillation (Rosenfeld et al., 1991; Rosenfeld et al., 1992),muscle injection (Ragot et al., 1993), peripheral intravenous injections(Herz and Gerard, 1993) and stereotactic inoculation into the brain (LeGal La Salle et al., 1993).

[0294] 4.15.2 Retroviruses

[0295] The retroviruses are a group of single-stranded RNA virusescharacterized by an ability to convert their RNA to double-stranded DNAin infected cells by a process of reverse-transcription (Coffin, 1990).The resulting DNA then stably integrates into cellular chromosomes as aprovirus and directs synthesis of viral proteins. The integrationresults in the retention of the viral gene sequences in the recipientcell and its descendants. The retroviral genome contains three genes,gag, pol, and env that code for capsid proteins, polymerase enzyme, andenvelope components, respectively. A sequence found upstream from thegag gene contains a signal for packaging of the genome into virions. Twolong terminal repeat (LTR) sequences are present at the 5′ and 3′ endsof the viral genome. These contain strong promoter and enhancersequences and are also required for integration in the host cell genome(Coffin, 1990).

[0296] In order to construct a retroviral vector, a nucleic acidencoding one or more oligonucleotide or polynucleotide sequences ofinterest is inserted into the viral genome in the place of certain viralsequences to produce a virus that is replication-defective. In order toproduce virions, a packaging cell line containing the gag, pol, and envgenes but without the LTR and packaging components is constructed (Mannet al., 1983). When a recombinant plasmid containing a cDNA, togetherwith the retroviral LTR and packaging sequences is introduced into thiscell line (by calcium phosphate precipitation for example), thepackaging sequence allows the RNA transcript of the recombinant plasmidto be packaged into viral particles, which are then secreted into theculture media (Nicolas and Rubenstein, 1988; Temin, 1986; Mann et al.,1983). The media containing the recombinant retroviruses is thencollected, optionally concentrated, and used for gene transfer.Retroviral vectors are able to infect a broad variety of cell types.However, integration and stable expression require the division of hostcells (Paskind et al., 1975).

[0297] A novel approach designed to allow specific targeting ofretrovirus vectors was recently developed based on the chemicalmodification of a retrovirus by the chemical addition of lactoseresidues to the viral envelope. This modification could permit thespecific infection of hepatocytes via sialoglycoprotein receptors.

[0298] A different approach to targeting of recombinant retroviruses wasdesigned in which biotinylated antibodies against a retroviral envelopeprotein and against a specific cell receptor were used. The antibodieswere coupled via the biotin components by using streptavidin (Roux etal., 1989). Using antibodies against major histocompatibility complexclass I and class II antigens, they demonstrated the infection of avariety of human cells that bore those surface antigens with anecotropic virus in vitro (Roux et al., 1989).

[0299] 4.15.3 Adeno-Associated Viruses

[0300] AAV (Ridgeway, 1988; Hermonat and Muzycska, 1984) is a parovirus,discovered as a contamination of adenoviral stocks. It is a ubiquitousvirus (antibodies are present in 85% of the US human population) thathas not been linked to any disease. It is also classified as adependovirus, because its replications is dependent on the presence of ahelper virus, such as adenovirus. Five serotypes have been isolated, ofwhich AAV-2 is the best characterized. AAV has a single-stranded linearDNA that is encapsidated into capsid proteins VP1, VP2 and VP3 to forman icosahedral virion of 20 to 24 nm in diameter (Muzyczka andMcLaughlin, 1988).

[0301] The AAV DNA is approximately 4.7 kilobases long. It contains twoopen reading frames and is flanked by two ITRs. There are two majorgenes in the AAV genome: rep and cap. The rep gene codes for proteinsresponsible for viral replications, whereas cap codes for capsid proteinVP 1-3. Each ITR forms a T-shaped hairpin structure. These terminalrepeats are the only essential cis components of the AAV for chromosomalintegration. Therefore, the AAV can be used as a vector with all viralcoding sequences removed and replaced by the cassette of genes fordelivery. Three viral promoters have been identified and named p5, p19,and p40, according to their map position. Transcription from p5 and p19results in production of rep proteins, and transcription from p40produces the capsid proteins (Hermonat and Muzyczka, 1984).

[0302] There are several factors that prompted researchers to study thepossibility of using rAAV as an expression vector. One is that therequirements for delivering a gene to integrate into the host chromosomeare surprisingly few. It is necessary to have the 145-bp ITRs, which areonly 6% of the AAV genome. This leaves room in the vector to assemble a4.5-kb DNA insertion. While this carrying capacity may prevent the AAVfrom delivering large genes, it is amply suited for delivering theantisense constructs of the present invention.

[0303] AAV is also a good choice of delivery vehicles due to its safety.There is a relatively complicated rescue mechanism: not only wild typeadenovirus but also AAV genes are required to mobilize rAAV. Likewise,AAV is not pathogenic and not associated with any disease. The removalof viral coding sequences minimizes immune reactions to viral geneexpression, and therefore, rAAV does not evoke an inflammatory response.

[0304] 4.15.4 Other Viral Vectors as Expression Constructs

[0305] Other viral vectors may be employed as expression constructs inthe present invention for the delivery of oligonucleotide orpolynucleotide sequences to a host cell. Vectors derived from virusessuch as vaccinia virus (Ridgeway, 1988; Coupar et al., 1988),lentiviruses, polio viruses and herpes viruses may be employed. Theyoffer several attractive features for various mammalian cells(Friedmann, 1989; Ridgeway, 1988; Coupar et al., 1988; Horwich et al.,1990).

[0306] With the recent recognition of defective hepatitis B viruses, newinsight was gained into the structure-function relationship of differentviral sequences. In vitro studies showed that the virus could retain theability for helper-dependent packaging and reverse transcription despitethe deletion of up to 80% of its genome (Horwich et al., 1990). Thissuggested that large portions of the genome could be replaced withforeign genetic material. The hepatotropism and persistence(integration) were particularly attractive properties for liver-directedgene transfer. Chang et al. (1991) introduced the chloramphenicolacetyltransferase (CAT) gene into duck hepatitis B virus genome in theplace of the polymerase, surface, and pre-surface coding sequences. Itwas cotransfected with wild-type virus into an avian hepatoma cell line.Culture media containing high titers of the recombinant virus were usedto infect primary duckling hepatocytes. Stable CAT gene expression wasdetected for at least 24 days after transfection (Chang et al., 1991).

[0307] 4.15.5 Non-Viral Vectors

[0308] In order to effect expression of the oligonucleotide orpolynucleotide sequences of the present invention, the expressionconstruct must be delivered into a cell. This delivery may beaccomplished in vitro, as in laboratory procedures for transformingcells lines, or in vivo or ex vivo, as in the treatment of certaindisease states. As described above, one preferred mechanism for deliveryis via viral infection where the expression construct is encapsulated inan infectious viral particle.

[0309] Once the expression construct has been delivered into the cellthe nucleic acid encoding the desired oligonucleotide or polynucleotidesequences may be positioned and expressed at different sites. In certainembodiments, the nucleic acid encoding the construct may be stablyintegrated into the genome of the cell. This integration may be in thespecific location and orientation via homologous recombination (genereplacement) or it may be integrated in a random, non-specific location(gene augmentation). In yet further embodiments, the nucleic acid may bestably maintained in the cell as a separate, episomal segment of DNA.Such nucleic acid segments or “episomes” encode sequences sufficient topermit maintenance and replication independent of or in synchronizationwith the host cell cycle. How the expression construct is delivered to acell and where in the cell the nucleic acid remains is dependent on thetype of expression construct employed.

[0310] In certain embodiments of the invention, the expression constructcomprising one or more oligonucleotide or polynucleotide sequences maysimply consist of naked recombinant DNA or plasmids. Transfer of theconstruct may be performed by any of the methods mentioned above whichphysically or chemically permeabilize the cell membrane. This isparticularly applicable for transfer in vitro but it may be applied toin vivo use as well. Dubensky et al. (1984) successfully injectedpolyomavirus DNA in the form of calcium phosphate precipitates intoliver and spleen of adult and newborn mice demonstrating active viralreplication and acute infection. Benvenisty and Reshef (1986) alsodemonstrated that direct intraperitoneal injection of calciumphosphate-precipitated plasmids results in expression of the transfectedgenes. It is envisioned that DNA encoding a gene of interest may also betransferred in a similar manner in vivo and express the gene product.

[0311] Another embodiment of the invention for transferring a naked DNAexpression construct into cells may involve particle bombardment. Thismethod depends on the ability to accelerate DNA-coated microprojectilesto a high velocity allowing them to pierce cell membranes and entercells without killing them (Klein et al., 1987). Several devices foraccelerating small particles have been developed. One such device relieson a high voltage discharge to generate an electrical current, which inturn provides the motive force (Yang et al., 1990). The microprojectilesused have consisted of biologically inert substances such as tungsten orgold beads.

[0312] Selected organs including the liver, skin, and muscle tissue ofrats and mice have been bombarded in vivo (Yang et al., 1990; Zelenin etal., 1991). This may require surgical exposure of the tissue or cells,to eliminate any intervening tissue between the gun and the targetorgan, i.e. ex vivo treatment. Again, DNA encoding a particular gene maybe delivered via this method and still be incorporated by the presentinvention.

[0313] 4.16 Antisense Oligonucleotides

[0314] The end result of the flow of genetic information is thesynthesis of protein. DNA is transcribed by polymerases into messengerRNA and translated on the ribosome to yield a folded, functionalprotein. Thus there are several steps along the route where proteinsynthesis can be inhibited. The native DNA segment coding for apolypeptide described herein, as all such mammalian DNA strands, has twostrands: a sense strand and an antisense strand held together byhydrogen bonding. The messenger RNA coding for polypeptide has the samenucleotide sequence as the sense DNA strand except that the DNAthymidine is replaced by uridine. Thus, synthetic antisense nucleotidesequences will bind to a mRNA and inhibit expression of the proteinencoded by that mRNA.

[0315] The targeting of antisense oligonucleotides to mRNA is thus onemechanism to shut down protein synthesis, and, consequently, representsa powerful and targeted therapeutic approach. For example, the synthesisof polygalactauronase and the muscarine type 2 acetylcholine receptorare inhibited by antisense oligonucleotides directed to their respectivemRNA sequences (U.S. Pat. No. 5,739,119 and U.S. Pat. No. 5,759,829,each specifically incorporated herein by reference in its entirety).Further, examples of antisense inhibition have been demonstrated withthe nuclear protein cyclin, the multiple drug resistance gene (MDG1),ICAM-1, E-selectin, STK-1, striatal GABA_(A) receptor and human EGF(Jaskulski et al., 1988; Vasanthakumar and Ahmed, 1989; Peris et al.,1998; U.S. Pat. No. 5,801,154; U.S. Pat. No. 5,789,573; U.S. Pat. No.5,718,709 and U.S. Pat. No. 5,610,288, each specifically incorporatedherein by reference in its entirety). Antisense constructs have alsobeen described that inhibit and can be used to treat a variety ofabnormal cellular proliferations, e.g. cancer (U.S. Pat. No. 5,747,470;U.S. Pat. No. 5,591,317 and U.S. Pat. No. 5,783,683, each specificallyincorporated herein by reference in its entirety).

[0316] Therefore, in exemplary embodiments, the invention providesoligonucleotide sequences that comprise all, or a portion of, anysequence that is capable of specifically binding to polynucleotidesequence described herein, or a complement thereof. In one embodiment,the antisense oligonucleotides comprise DNA or derivatives thereof. Inanother embodiment, the oligonucleotides comprise RNA or derivativesthereof. In a third embodiment, the oligonucleotides are modified DNAscomprising a phosphorothioated modified backbone. In a fourthembodiment, the oligonucleotide sequences comprise peptide nucleic acidsor derivatives thereof. In each case, preferred compositions comprise asequence region that is complementary, and more preferablysubstantially-complementary, and even more preferably, completelycomplementary to one or more portions of polynucleotides disclosedherein.

[0317] Selection of antisense compositions specific for a given genesequence is based upon analysis of the chosen target sequence (i.e. inthese illustrative examples the rat and human sequences) anddetermination of secondary structure, Tm, binding energy, relativestability, and antisense compositions were selected based upon theirrelative inability to form dimers, hairpins, or other secondarystructures that would reduce or prohibit specific binding to the targetmRNA in a host cell.

[0318] Highly preferred target regions of the mRNA, are those which areat or near the AUG translation initiation codon, and those sequenceswhich were substantially complementary to 5′ regions of the mRNA. Thesesecondary structure analyses and target site selection considerationswere performed using v.4 of the OLIGO primer analysis software (Rychlik,1997) and the BLASTN 2.0.5 algorithm software (Altschul et al., 1997).

[0319] The use of an antisense delivery method employing a short peptidevector, termed MPG (27 residues), is also contemplated. The MPG peptidecontains a hydrophobic domain derived from the fusion sequence of HIVgp41 and a hydrophilic domain from the nuclear localization sequence ofSV40 T-antigen (Morris et al., 1997). It has been demonstrated thatseveral molecules of the MPG peptide coat the antisense oligonucleotidesand can be delivered into cultured mammalian cells in less than 1 hourwith relatively high efficiency (90%). Further, the interaction with MPGstrongly increases both the stability of the oligonucleotide to nucleaseand the ability to cross the plasma membrane (Morris et al., 1997).

[0320] 4.17 Ribozymes

[0321] Although proteins traditionally have been used for catalysis ofnucleic acids, another class of macromolecules has emerged as useful inthis endeavor. Ribozymes are RNA-protein complexes that cleave nucleicacids in a site-specific fashion. Ribozymes have specific catalyticdomains that possess endonuclease activity (Kim and Cech, 1987; Gerlachet al., 1987; Forster and Symons, 1987). For example, a large number ofribozymes accelerate phosphoester transfer reactions with a high degreeof specificity, often cleaving only one of several phosphoesters in anoligonucleotide substrate (Cech et al., 1981; Michel and Westhof, 1990;Reinhold-Hurek and Shub, 1992). This specificity has been attributed tothe requirement that the substrate bind via specific base-pairinginteractions to the internal guide sequence (“IGS”) of the ribozymeprior to chemical reaction.

[0322] Ribozyme catalysis has primarily been observed as part ofsequence-specific cleavage/ligation reactions involving nucleic acids(Joyce, 1989; Cech et al., 1981). For example, U.S. Pat. No. 5,354,855(specifically incorporated herein by reference) reports that certainribozymes can act as endonucleases with a sequence specificity greaterthan that of known ribonucleases and approaching that of the DNArestriction enzymes. Thus, sequence-specific ribozyme-mediatedinhibition of gene expression may be particularly suited to therapeuticapplications (Scanlon et al., 1991; Sarver et al., 1990). Recently, itwas reported that ribozymes elicited genetic changes in some cells linesto which they were applied; the altered genes included the oncogenesH-ras, c-fos and genes of HIV. Most of this work involved themodification of a target mRNA, based on a specific mutant codon that iscleaved by a specific ribozyme.

[0323] Six basic varieties of naturally-occurring enzymatic RNAs areknown presently. Each can catalyze the hydrolysis of RNA phosphodiesterbonds in trans (and thus can cleave other RNA molecules) underphysiological conditions. In general, enzymatic nucleic acids act byfirst binding to a target RNA. Such binding occurs through the targetbinding portion of a enzymatic nucleic acid which is held in closeproximity to an enzymatic portion of the molecule that acts to cleavethe target RNA. Thus, the enzymatic nucleic acid first recognizes andthen binds a target RNA through complementary base-pairing, and oncebound to the correct site, acts enzymatically to cut the target RNA.Strategic cleavage of such a target RNA will destroy its ability todirect synthesis of an encoded protein. After an enzymatic nucleic acidhas bound and cleaved its RNA target, it is released from that RNA tosearch for another target and can repeatedly bind and cleave newtargets.

[0324] The enzymatic nature of a ribozyme is advantageous over manytechnologies, such as antisense technology (where a nucleic acidmolecule simply binds to a nucleic acid target to block its translation)since the concentration of ribozyme necessary to affect a therapeutictreatment is lower than that of an antisense oligonucleotide. Thisadvantage reflects the ability of the ribozyme to act enzymatically.Thus, a single ribozyme molecule is able to cleave many molecules oftarget RNA. In addition, the ribozyme is a highly specific inhibitor,with the specificity of inhibition depending not only on the basepairing mechanism of binding to the target RNA, but also on themechanism of target RNA cleavage. Single mismatches, orbase-substitutions, near the site of cleavage can completely eliminatecatalytic activity of a ribozyme. Similar mismatches in antisensemolecules do not prevent their action (Woolf et al., 1992). Thus, thespecificity of action of a ribozyme is greater than that of an antisenseoligonucleotide binding the same RNA site.

[0325] The enzymatic nucleic acid molecule may be formed in ahammerhead, hairpin, a hepatitis δ virus, group I intron or RNaseP RNA(in association with an RNA guide sequence) or Neurospora VS RNA motif.Examples of hammerhead motifs are described by Rossi et al. (1992).Examples of hairpin motifs are described by Hampel et al. (Eur. Pat.Appl. Publ. No. EP 0360257), Hampel and Tritz (1989), Hampel et al.(1990) and U.S. Pat. No. 5,631,359 (specifically incorporated herein byreference). An example of the hepatitis 8 virus motif is described byPerrotta and Been (1992); an example of the RNaseP motif is described byGuerrier-Takada et al. (1983); Neurospora VS RNA ribozyme motif isdescribed by Collins (Saville and Collins, 1990; Saville and Collins,1991; Collins and Olive, 1993); and an example of the Group I intron isdescribed in (U.S. Pat. No. 4,987,071, specifically incorporated hereinby reference). All that is important in an enzymatic nucleic acidmolecule of this invention is that it has a specific substrate bindingsite which is complementary to one or more of the target gene RNAregions, and that it have nucleotide sequences within or surroundingthat substrate binding site which impart an RNA cleaving activity to themolecule. Thus the ribozyme constructs need not be limited to specificmotifs mentioned herein.

[0326] In certain embodiments, it may be important to produce enzymaticcleaving agents which exhibit a high degree of specificity for the RNAof a desired target, such as one of the sequences disclosed herein. Theenzymatic nucleic acid molecule is preferably targeted to a highlyconserved sequence region of a target mRNA. Such enzymatic nucleic acidmolecules can be delivered exogenously to specific cells as required.Alternatively, the ribozymes can be expressed from DNA or RNA vectorsthat are delivered to specific cells.

[0327] Small enzymatic nucleic acid motifs (e.g., of the hammerhead orthe hairpin structure) may also be used for exogenous delivery. Thesimple structure of these molecules increases the ability of theenzymatic nucleic acid to invade targeted regions of the mRNA structure.Alternatively, catalytic RNA molecules can be expressed within cellsfrom eukaryotic promoters (e.g., Scanlon et al, 1991; Kashani-Sabet etal., 1992; Dropulic et al., 1992; Weerasinghe et al., 1991; Ojwang etal., 1992; Chen et al., 1992; Sarver et al., 1990). Those skilled in theart realize that any ribozyme can be expressed in eukaryotic cells fromthe appropriate DNA vector. The activity of such ribozymes can beaugmented by their release from the primary transcript by a secondribozyme (Int. Pat. Appl. Publ. No. WO 93/23569, and Int. Pat. Appl.Publ. No. WO 94/02595, both hereby incorporated by reference; Ohkawa etal., 1992; Taira et al., 1991; and Ventura et al., 1993).

[0328] Ribozymes may be added directly, or can be complexed withcationic lipids, lipid complexes, packaged within liposomes, orotherwise delivered to target cells. The RNA or RNA complexes can belocally administered to relevant tissues ex vivo, or in vivo throughinjection, aerosol inhalation, infusion pump or stent, with or withouttheir incorporation in biopolymers.

[0329] Ribozymes may be designed as described in Int. Pat. Appl. Publ.No. WO 93/23569 and Int. Pat. Appl. Publ. No. WO 94/02595, eachspecifically incorporated herein by reference) and synthesized to betested in vitro and in vivo, as described. Such ribozymes can also beoptimized for delivery. While specific examples are provided, those inthe art will recognize that equivalent RNA targets in other species canbe utilized when necessary.

[0330] Hammerhead or hairpin ribozymes may be individually analyzed bycomputer folding (Jaeger et al., 1989) to assess whether the ribozymesequences fold into the appropriate secondary structure. Those ribozymeswith unfavorable intramolecular interactions between the binding armsand the catalytic core are eliminated from consideration. Varyingbinding arm lengths can be chosen to optimize activity. Generally, atleast 5 or so bases on each arm are able to bind to, or otherwiseinteract with, the target RNA.

[0331] Ribozymes of the hammerhead or hairpin motif may be designed toanneal to various sites in the mRNA message, and can be chemicallysynthesized. The method of synthesis used follows the procedure fornormal RNA synthesis as described in Usman et al. (1987) and in Scaringeet al. (1990) and makes use of common nucleic acid protecting andcoupling groups, such as dimethoxytrityl at the 5′-end, andphosphoramidites at the 3′-end. Average stepwise coupling yields aretypically >98%. Hairpin ribozymes may be synthesized in two parts andannealed to reconstruct an active ribozyme (Chowrira and Burke, 1992).Ribozymes may be modified extensively to enhance stability bymodification with nuclease resistant groups, for example, 2′-amino,2′-C-allyl, 2′-flouro, 2′-o-methyl, 2′-H (for a review see e.g., Usmanand Cedergren, 1992). Ribozymes may be purified by gel electrophoresisusing general methods or by high pressure liquid chromatography andresuspended in water.

[0332] Ribozyme activity can be optimized by altering the length of theribozyme binding arms, or chemically synthesizing ribozymes withmodifications that prevent their degradation by serum ribonucleases (seee.g., Int. Pat. Appl. Publ. No. WO 92/07065; Perrault et al, 1990;Pieken et al., 1991; Usman and Cedergren, 1992; Int. Pat. Appl. Publ.No. WO 93/15187; Int. Pat. Appl. Publ. No. WO 91/03162; Eur. Pat. Appl.Publ. No.92110298.4; U.S. Pat. No. 5,334,711; and Int. Pat. Appl. Publ.No. WO 94/13688, which describe various chemical modifications that canbe made to the sugar moieties of enzymatic RNA molecules), modificationswhich enhance their efficacy in cells, and removal of stem II bases toshorten RNA synthesis times and reduce chemical requirements.

[0333] Sullivan et al. (Int. Pat. Appl. Publ. No. WO 94/02595) describesthe general methods for delivery of enzymatic RNA molecules. Ribozymesmay be administered to cells by a variety of methods known to thosefamiliar to the art, including, but not restricted to, encapsulation inliposomes, by iontophoresis, or by incorporation into other vehicles,such as hydrogels, cyclodextrins, biodegradable nanocapsules, andbioadhesive microspheres. For some indications, ribozymes may bedirectly delivered ex vivo to cells or tissues with or without theaforementioned vehicles. Alternatively, the RNA/vehicle combination maybe locally delivered by direct inhalation, by direct injection or by useof a catheter, infusion pump or stent. Other routes of delivery include,but are not limited to, intravascular, intramuscular, subcutaneous orjoint injection, aerosol inhalation, oral (tablet or pill form),topical, systemic, ocular, intraperitoneal and/or intrathecal delivery.More detailed descriptions of ribozyme delivery and administration areprovided in Int. Pat. Appl. Publ. No. WO 94/02595 and Int. Pat. Appl.Publ. No. WO 93/23569, each specifically incorporated herein byreference.

[0334] Another means of accumulating high concentrations of aribozyme(s) within cells is to incorporate the ribozyme-encodingsequences into a DNA expression vector. Transcription of the ribozymesequences are driven from a promoter for eukaryotic RNA polymerase I(pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III).Transcripts from pol II or pol III promoters will be expressed at highlevels in all cells; the levels of a given pol II promoter in a givencell type will depend on the nature of the gene regulatory sequences(enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerasepromoters may also be used, providing that the prokaryotic RNApolymerase enzyme is expressed in the appropriate cells (Elroy-Stein andMoss, 1990; Gao and Huang, 1993; Lieber et al., 1993; Zhou et al.,1990). Ribozymes expressed from such promoters can function in mammaliancells (e.g. Kashani-Saber et al., 1992; Ojwang et al., 1992; Chen etal., 1992; Yu et al., 1993; L'Huillier et al., 1992; Lisziewicz et al.,1993). Such transcription units can be incorporated into a variety ofvectors for introduction into mammalian cells, including but notrestricted to, plasmid DNA vectors, viral DNA vectors (such asadenovirus or adeno-associated vectors), or viral RNA vectors (such asretroviral, semliki forest virus, sindbis virus vectors).

[0335] Ribozymes may be used as diagnostic tools to examine geneticdrift and mutations within diseased cells. They can also be used toassess levels of the target RNA molecule. The close relationship betweenribozyme activity and the structure of the target RNA allows thedetection of mutations in any region of the molecule which alters thebase-pairing and three-dimensional structure of the target RNA. By usingmultiple ribozymes, one may map nucleotide changes which are importantto RNA structure and function in vitro, as well as in cells and tissues.Cleavage of target RNAs with ribozymes may be used to inhibit geneexpression and define the role (essentially) of specified gene productsin the progression of disease. In this manner, other genetic targets maybe defined as important mediators of the disease. These studies willlead to better treatment of the disease progression by affording thepossibility of combinational therapies (e.g., multiple ribozymestargeted to different genes, ribozymes coupled with known small moleculeinhibitors, or intermittent treatment with combinations of ribozymesand/or other chemical or biological molecules). Other in vitro uses ofribozymes are well known in the art, and include detection of thepresence of mRNA associated with an IL-5 related condition. Such RNA isdetected by determining the presence of a cleavage product aftertreatment with a ribozyme using standard methodology.

[0336] 4.18 Peptide Nucleic Acids

[0337] In certain embodiments, the inventors contemplate the use ofpeptide nucleic acids (PNAs) in the practice of the methods of theinvention. PNA is a DNA mimic in which the nucleobases are attached to apseudopeptide backbone (Good and Nielsen, 1997). PNA is able to beutilized in a number methods that traditionally have used RNA or DNA.Often PNA sequences perform better in techniques than the correspondingRNA or DNA sequences and have utilities that are not inherent to RNA orDNA. A review of PNA including methods of making, characteristics of,and methods of using, is provided by Corey (1997) and is incorporatedherein by reference. As such, in certain embodiments, one may preparePNA sequences that are complementary to one or more portions of the ACEmRNA sequence, and such PNA compositions may be used to regulate, alter,decrease, or reduce the translation of ACE-specific mRNA, and therebyalter the level of ACE activity in a host cell to which such PNAcompositions have been administered.

[0338] PNAs have 2-aminoethyl-glycine linkages replacing the normalphosphodiester backbone of DNA (Nielsen et al., 1991; Hanvey et al.,1992; Hyrup and Nielsen, 1996; Neilsen, 1996). This chemistry has threeimportant consequences: firstly, in contrast to DNA or phosphorothioateoligonucleotides, PNAs are neutral molecules; secondly, PNAs areachiral, which avoids the need to develop a stereoselective synthesis;and thirdly, PNA synthesis uses standard Boc (Dueholm et al., 1994) orFmoc (Thomson et al., 1995) protocols for solid-pliase peptidesynthesis, although other methods, including a modified Merrifieldmethod, have been used (Christensen et al., 1995).

[0339] PNA monomers or ready-made oligomers are commercially availablefrom PerSeptive Biosystems (Framingham, Mass.). PNA syntheses by eitherBoc or Fmoc protocols are straightforward using manual or automatedprotocols (Norton et al., 1995). The manual protocol lends itself to theproduction of chemically modified PNAs or the simultaneous synthesis offamilies of closely related PNAs.

[0340] As with peptide synthesis, the success of a particular PNAsynthesis will depend on the properties of the chosen sequence. Forexample, while in theory PNAs can incorporate any combination ofnucleotide bases, the presence of adjacent purines can lead to deletionsof one or more residues in the product. In expectation of thisdifficulty, it is suggested that, in producing PNAs with adjacentpurines, one should repeat the coupling of residues likely to be addedinefficiently. This should be followed by the purification of PNAs byreverse-phase high-pressure liquid chromatography (Norton et al., 1995)providing yields and purity of product similar to those observed duringthe synthesis of peptides.

[0341] Modifications of PNAs for a given application may be accomplishedby coupling amino acids during solid-phase synthesis or by attachingcompounds that contain a carboxylic acid group to the exposed N-terminalamine. Alternatively, PNAs can be modified after synthesis by couplingto an introduced lysine or cysteine. The ease with which PNAs can bemodified facilitates optimization for better solubility or for specificfunctional requirements. Once synthesized, the identity of PNAs andtheir derivatives can be confirmed by mass spectrometry. Several studieshave made and utilized modifications of PNAs (Norton et al., 1995;Haaima et al., 1996; Stetsenko et al., 1996; Petersen et al., 1995;Ulmann et al., 1996; Koch et al., 1995; Orum et al., 1995; Footer etal., 1996; Griffith et al., 1995; Kremsky et al., 1996; Pardridge etal., 1995; Boffa et al., 1995; Landsdorp et al., 1996;Gambacorti-Passerini et al., 1996; Armitage et al., 1997; Seeger et al.,1997; Ruskowski et al., 1997). U.S. Pat. No. 5,700,922 discussesPNA-DNA-PNA chimeric molecules and their uses in diagnostics, modulatingprotein in organisms, and treatment of conditions susceptible totherapeutics.

[0342] In contrast to DNA and RNA, which contain negatively chargedlinkages, the PNA backbone is neutral. In spite of this dramaticalteration, PNAs recognize complementary DNA and RNA by Watson-Crickpairing (Egholm et al., 1993), validating the initial modeling byNielsen et al. (1991). PNAs lack 3′ to 5′ polarity and can bind ineither parallel or anti-parallel fashion, with the anti-parallel modebeing preferred (Egholm et al., 1993).

[0343] Hybridization of DNA oligonucleotides to DNA and RNA isdestabilized by electrostatic repulsion between the negatively chargedphosphate backbones of the complementary strands. By contrast, theabsence of charge repulsion in PNA-DNA or PNA-RNA duplexes increases themelting temperature (T_(m)) and reduces the dependence of T_(m) on theconcentration of mono- or divalent cations (Nielsen et al., 1991). Theenhanced rate and affinity of hybridization are significant because theyare responsible for the surprising ability of PNAs to perform strandinvasion of complementary sequences within relaxed double-stranded DNA.In addition, the efficient hybridization at inverted repeats suggeststhat PNAs can recognize secondary structure effectively withindouble-stranded DNA. Enhanced recognition also occurs with PNAsimmobilized on surfaces, and Wang et al. have shown that support-boundPNAs can be used to detect hybridization events (Wang et al., 1996).

[0344] One might expect that tight binding of PNAs to complementarysequences would also increase binding to similar (but not identical)sequences, reducing the sequence specificity of PNA recognition. As withDNA hybridization, however, selective recognition can be achieved bybalancing oligomer length and incubation temperature. Moreover,selective hybridization of PNAs is encouraged by PNA-DNA hybridizationbeing less tolerant of base mismatches than DNA-DNA hybridization. Forexample, a single mismatch within a 16 bp PNA-DNA duplex can reduce theT_(m) by up to 15° C. (Egholm et al., 1993). This high level ofdiscrimination has allowed the development of several PNA-basedstrategies for the analysis of point mutations (Wang et al., 1996;Carlsson et al., 1996; Thiede et al., 1996; Webb and Hurskainen, 1996;Perry-O'Keefe et al., 1996).

[0345] High-affinity binding provides clear advantages for molecularrecognition and the development of new applications for PNAs. Forexample, 11-13 nucleotide PNAs inhibit the activity of telomerase, aribonucleo-protein that extends telomere ends using an essential RNAtemplate, while the analogous DNA oligomers do not (Norton et al.,1996).

[0346] Neutral PNAs are more hydrophobic than analogous DNA oligomers,and this can lead to difficulty solubilizing them at neutral pH,especially if the PNAs have a high purine content or if they have thepotential to form secondary structures. Their solubility can be enhancedby attaching one or more positive charges to the PNA termini (Nielsen etal., 1991).

[0347] Findings by Allfrey and colleagues suggest that strand invasionwill occur spontaneously at sequences within chromosomal DNA (Boffa etal., 1995; Boffa et al., 1996). These studies targeted PNAs to tripletrepeats of the nucleotides CAG and used this recognition to purifytranscriptionally active DNA (Boffa et al., 1995) and to inhibittranscription (Boffa et al., 1996). This result suggests that if PNAscan be delivered within cells then they will have the potential to begeneral sequence-specific regulators of gene expression. Studies andreviews concerning the use of PNAs as antisense and anti-gene agentsinclude Nielsen et al. (1993b), Hanvey et al. (1992), and Good andNielsen (1997). Koppelhus et al. (1997) have used PNAs to inhibit HIV-1inverse transcription, showing that PNAs may be used for antiviraltherapies.

[0348] Methods of characterizing the antisense binding properties ofPNAs are discussed in Rose (1993) and Jensen et al. (1997). Rose usescapillary gel electrophoresis to determine binding of PNAs to theircomplementary oligonucleotide, measuring the relative binding kineticsand stoichiometry. Similar types of measurements were made by Jensen etal. using BIAcore™ technology.

[0349] Other applications of PNAs include use in DNA strand invasion(Nielsen et al., 1991), antisense inhibition (Hanvey et al., 1992),mutational analysis (Orum et al., 1993), enhancers of transcription(Mollegaard et al., 1994), nucleic acid purification (Orum et al.,1995), isolation of transcriptionally active genes (Boffa et al., 1995),blocking of transcription factor binding (Vickers et al., 1995), genomecleavage (Veselkov et al., 1996), biosensors (Wang et al., 1996), insitu hybridization (Thisted et al., 1996), and in a alternative toSouthern blotting (Perry-O'Keefe, 1996).

[0350] 4.19 Polypeptide, Peptides and Peptide Variants

[0351] The present invention, in other aspects, provides polypeptidecompositions. Generally, a polypeptide of the invention will be anisolated polypeptide (or an epitope, variant, or active fragmentthereof) derived from a mammalian species. Preferably, the polypeptideis encoded by a polynucleotide sequence disclosed herein or a sequencewhich hybridizes under moderately stringent conditions to apolynucleotide sequence disclosed herein. Alternatively, the polypeptidemay be defined as a polypeptide which comprises a contiguous amino acidsequence from an amino acid sequence disclosed herein, or whichpolypeptide comprises an entire amino acid sequence disclosed herein.

[0352] In the present invention, a polypeptide composition is alsounderstood to comprise one or more polypeptides that are immunologicallyreactive with antibodies generated against a polypeptide of theinvention, particularly a polypeptide having the amino acid sequenceencoded by the polynucleotides disclosed in SEQ ID NO:9598-9610, or toactive fragments, or to variants or biological functional equivalentsthereof.

[0353] Likewise, a polypeptide composition of the present invention isunderstood to comprise one or more polypeptides that are capable ofeliciting antibodies that are immunologically reactive with one or morepolypeptides encoded by one or more contiguous nucleic acid sequencescontained in SEQ ID NO:9598-9610, or to active fragments, or to variantsthereof, or to one or more nucleic acid sequences which hybridize to oneor more of these sequences under conditions of moderate to highstringency. Particularly illustrative polypeptides include the aminoacid sequences encoded by polynucleotides disclosed in SEQ IDNO:9598-9610.

[0354] As used herein, an active fragment of a polypeptide includes awhole or a portion of a polypeptide which is modified by conventionaltechniques, e.g., mutagenesis, or by addition, deletion, orsubstitution, but which active fragment exhibits substantially the samestructure function, antigenicity, etc., as a polypeptide as describedherein.

[0355] In certain illustrative embodiments, the polypeptides of theinvention will comprise at least an immunogenic portion of ahematological malignancy-related tumor protein or a variant thereof, asdescribed herein. As noted above, a “hematological malignancy-relatedtumor protein” is a protein that is expressed by hematologicalmalignancy-related tumor cells. Proteins that are hematologicalmalignancy-related tumor proteins also react detectably within animmunoassay (such as an ELISA) with antisera from a patient withhematological malignancy. Polypeptides as described herein may be of anylength. Additional sequences derived from the native protein and/orheterologous sequences may be present, and such sequences may (but neednot) possess further immunogenic or antigenic properties.

[0356] An “immunogenic portion,” as used herein is a portion of aprotein that is recognized (i.e., specifically bound) by a B-cell and/orT-cell surface antigen receptor. Such immunogenic portions generallycomprise at least 5 amino acid residues, more preferably at least 10,and still more preferably at least 20 amino acid residues of ahematological malignancy-related tumor protein or a variant thereof.Certain preferred immunogenic portions include peptides in which anN-terminal leader sequence and/or transmembrane domain have beendeleted. Other preferred immunogenic portions may contain a small N-and/or C-terminal deletion (e.g., 1-30 amino acids, preferably 5-15amino acids), relative to the mature protein.

[0357] Immunogenic portions may generally be identified using well knowntechniques, such as those summarized in Paul, Fundamental Immunology,3rd ed., 243-247 (Raven Press, 1993) and references cited therein. Suchtechniques include screening polypeptides for the ability to react withantigen-specific antibodies, antisera and/or T-cell lines or clones. Asused herein, antisera and antibodies are “antigen-specific” if theyspecifically bind to an antigen (i.e., they react with the protein in anELISA or other immunoassay, and do not react detectably with unrelatedproteins). Such antisera and antibodies may be prepared as describedherein, and using well known techniques. An immunogenic portion of anative hematological malignancy-related tumor protein is a portion thatreacts with such antisera and/or T-cells at a level that is notsubstantially less than the reactivity of the full length polypeptide(e.g., in an ELISA and/or T-cell reactivity assay). Such immunogenicportions may react within such assays at a level that is similar to orgreater than the reactivity of the full length polypeptide. Such screensmay generally be performed using methods well known to those of ordinaryskill in the art, such as those described in Harlow and Lane,Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988.For example, a polypeptide may be immobilized on a solid support andcontacted with patient sera to allow binding of antibodies within thesera to the immobilized polypeptide. Unbound sera may then be removedand bound antibodies detected using, for example, ¹²⁵I-labeled ProteinA.

[0358] As noted above, a composition may comprise a variant of a nativehematological malignancy-related tumor protein. A polypeptide “variant,”as used herein, is a polypeptide that differs from a nativehematological malignancy-related tumor protein in one or moresubstitutions, deletions, additions and/or insertions, such that theimmunogenicity of the polypeptide is not substantially diminished. Inother words, the ability of a variant to react with antigen-specificantisera may be enhanced or unchanged, relative to the native protein,or may be diminished by less than 50%, and preferably less than 20%,relative to the native protein. Such variants may generally beidentified by modifying one of the above polypeptide sequences andevaluating the reactivity of the modified polypeptide withantigen-specific antibodies or antisera as described herein. Preferredvariants include those in which one or more portions, such as anN-terminal leader sequence or transmembrane domain, have been removed.Other preferred variants include variants in which a small portion(e.g., 1-30 amino acids, preferably 5-15 amino acids) has been removedfrom the N- and/or C-terminal of the mature protein.

[0359] Polypeptide variants encompassed by the present invention includethose exhibiting at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% or more identity (determined asdescribed above) to the polypeptides disclosed herein.

[0360] Preferably, a variant contains conservative substitutions. A“conservative substitution” is one in which an amino acid is substitutedfor another amino acid that has similar properties, such that oneskilled in the art of peptide chemistry would expect the secondarystructure and hydropathic nature of the polypeptide to be substantiallyunchanged. Amino acid substitutions may generally be made on the basisof similarity in polarity, charge, solubility, hydrophobicity,hydrophilicity and/or the amphipathic nature of the residues. Forexample, negatively charged amino acids include aspartic acid andglutamic acid; positively charged amino acids include lysine andarginine; and amino acids with uncharged polar head groups havingsimilar hydrophilicity values include leucine, isoleucine and valine;glycine and alanine; asparagine and glutamine; and serine, threonine,phenylalanine and tyrosine. Other groups of amino acids that mayrepresent conservative changes include: (1) ala, pro, gly, glu, asp,gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala,phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also,or alternatively, contain nonconservative changes. In a preferredembodiment, variant polypeptides differ from a native sequence bysubstitution, deletion or addition of five amino acids or fewer.Variants may also (or alternatively) be modified by, for example, thedeletion or addition of amino acids that have minimal influence on theimmunogenicity, secondary structure and hydropathic nature of thepolypeptide.

[0361] As noted above, polypeptides may comprise a signal (or leader)sequence at the N-terminal end of the protein, which co-translationallyor post-translationally directs transfer of the protein. The polypeptidemay also be conjugated to a linker or other sequence for ease ofsynthesis, purification or identification of the polypeptide (e.g.,poly-His), or to enhance binding of the polypeptide to a solid support.For example, a polypeptide may be conjugated to an immunoglobulin Fcregion.

[0362] Polypeptides may be prepared using any of a variety of well knowntechniques. Recombinant polypeptides encoded by DNA sequences asdescribed above may be readily prepared from the DNA sequences using anyof a variety of expression vectors known to those of ordinary skill inthe art. Expression may be achieved in any appropriate host cell thathas been transformed or transfected with an expression vector containinga DNA molecule that encodes a recombinant polypeptide. Suitable hostcells include prokaryotes, yeast, and higher eukaryotic cells, such asmammalian cells and plant cells. Preferably, the host cells employed areE. coli, yeast or a mammalian cell line such as COS or CHO. Supernatantsfrom suitable host/vector systems which secrete recombinant protein orpolypeptide into culture media may be first concentrated using acommercially available filter. Following concentration, the concentratemay be applied to a suitable purification matrix such as an affinitymatrix or an ion exchange resin. Finally, one or more reverse phase HPLCsteps can be employed to further purify a recombinant polypeptide.

[0363] Portions and other variants having less than about 100 aminoacids, and generally less than about 50 amino acids, may also begenerated by synthetic means, using techniques well known to those ofordinary skill in the art. For example, such polypeptides may besynthesized using any of the commercially available solid-phasetechniques, such as the Merrifield solid-phase synthesis method, whereamino acids are sequentially added to a growing amino acid chain. SeeMerrifield, J. Am. Chem. Soc. 85:2149-2146, 1963. Equipment forautomated synthesis of polypeptides is commercially available fromsuppliers such as Perkin Elmer/Applied BioSystems Division (Foster City,Calif.), and may be operated according to the manufacturer'sinstructions.

[0364] Within certain specific embodiments, a polypeptide may be afusion protein that comprises multiple polypeptides as described herein,or that comprises at least one polypeptide as described herein and anunrelated sequence, such as a known tumor protein. A fusion partner may,for example, assist in providing T helper epitopes (an immunologicalfusion partner), preferably T helper epitopes recognized by humans, ormay assist in expressing the protein (an expression enhancer) at higheryields than the native recombinant protein. Certain preferred fusionpartners are both immunological and expression enhancing fusionpartners. Other fusion partners may be selected so as to increase thesolubility of the protein or to enable the protein to be targeted todesired intracellular compartments. Still further fusion partnersinclude affinity tags, which facilitate purification of the protein.

[0365] Fusion proteins may generally be prepared using standardtechniques, including chemical conjugation. Preferably, a fusion proteinis expressed as a recombinant protein, allowing the production ofincreased levels, relative to a non-fused protein, in an expressionsystem. Briefly, DNA sequences encoding the polypeptide components maybe assembled separately, and ligated into an appropriate expressionvector. The 3′ end of the DNA sequence encoding one polypeptidecomponent is ligated, with or without a peptide linker, to the 5′ end ofa DNA sequence encoding the second polypeptide component so that thereading frames of the sequences are in phase. This permits translationinto a single fusion protein that retains the biological activity ofboth component polypeptides.

[0366] A peptide linker sequence may be employed to separate the firstand second polypeptide components by a distance sufficient to ensurethat each polypeptide folds into its secondary and tertiary structures.Such a peptide linker sequence is incorporated into the fusion proteinusing standard techniques well known in the art. Suitable peptide linkersequences may be chosen based on the following factors: (1) theirability to adopt a flexible extended conformation; (2) their inabilityto adopt a secondary structure that could interact with functionalepitopes on the first and second polypeptides; and (3) the lack ofhydrophobic or charged residues that might react with the polypeptidefunctional epitopes. Preferred peptide linker sequences contain Gly, Asnand Ser residues. Other near neutral amino acids, such as Thr and Alamay also be used in the linker sequence. Amino acid sequences which maybe usefully employed as linkers include those disclosed in Maratea etal., Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA83:8258-8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180.The linker sequence may generally be from 1 to about 50 amino acids inlength. Linker sequences are not required when the first and secondpolypeptides have non-essential N-terminal amino acid regions that canbe used to separate the functional domains and prevent stericinterference.

[0367] The ligated DNA sequences are operably linked to suitabletranscriptional or translational regulatory elements. The regulatoryelements responsible for expression of DNA are located only 5′ to theDNA sequence encoding the first polypeptides. Similarly, stop codonsrequired to end translation and transcription termination signals areonly present 3′ to the DNA sequence encoding the second polypeptide.

[0368] Fusion proteins are also provided. Such proteins comprise apolypeptide as described herein together with an unrelated immunogenicprotein. Preferably the immunogenic protein is capable of eliciting arecall response. Examples of such proteins include tetanus, tuberculosisand hepatitis proteins (see, for example, Stoute et al. New Engl. J.Med., 336:86-91, 1997).

[0369] Within preferred embodiments, an immunological fusion partner isderived from protein D, a surface protein of the gram-negative bacteriumHaemophilus influenza B (WO 91/18926). Preferably, a protein Dderivative comprises approximately the first third of the protein (e.g.,the first N-terminal 100-110 amino acids), and a protein D derivativemay be lipidated. Within certain preferred embodiments, the first 109residues of a Lipoprotein D fusion partner is included on the N-terminusto provide the polypeptide with additional exogenous T-cell epitopes andto increase the expression level in E. coli (thus functioning as anexpression enhancer). The lipid tail ensures optimal presentation of theantigen to antigen presenting cells. Other fusion partners include thenon-structural protein from influenzae virus, NS1 (hemagglutinin).Typically, the N-terminal 81 amino acids are used, although differentfragments that include T-helper epitopes may be used.

[0370] In another embodiment, the immunological fusion partner is theprotein known as LYTA, or a portion thereof (preferably a C-terminalportion). LYTA is derived from Streptococcus pneumoniae, whichsynthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encodedby the LytA gene; Gene 43:265-292, 1986). LYTA is an autolysin thatspecifically degrades certain bonds in the peptidoglycan backbone. TheC-terminal domain of the LYTA protein is responsible for the affinity tothe choline or to some choline analogues such as DEAE. This property hasbeen exploited for the development of E. coli C-LYTA expressing plasmidsuseful for expression of fusion proteins. Purification of hybridproteins containing the C-LYTA fragment at the amino terminus has beendescribed (see Biotechnology 10:795-798, 1992). Within a preferredembodiment, a repeat portion of LYTA may be incorporated into a fusionprotein. A repeat portion is found in the C-terminal region starting atresidue 178. A particularly preferred repeat portion incorporatesresidues 188-305.

[0371] In general, polypeptides (including fusion proteins) andpolynucleotides as described herein are isolated. An “isolated”polypeptide or polynucleotide is one that is removed from its originalenvironment. For example, a naturally-occurring protein is isolated ifit is separated from some or all of the coexisting materials in thenatural system. Preferably, such polypeptides are at least about 90%pure, more preferably at least about 95% pure and most preferably atleast about 99% pure. A polynucleotide is considered to be isolated if,for example, it is cloned into a vector that is not a part of thenatural environment.

[0372] 4.20 Binding Agents

[0373] The present invention further employs agents, such as antibodiesand antigen-binding fragments thereof, that specifically bind to ahematological malignancy-related antigen. As used herein, an antibody,or antigen-binding fragment thereof, is said to “specifically bind” to ahematological malignancy-related antigen if it reacts at a detectablelevel (within, for example, an ELISA) with, and does not reactdetectably with unrelated proteins under similar conditions. As usedherein, “binding” refers to a noncovalent association between twoseparate molecules such that a complex is formed. The ability to bindmay be evaluated by, for example, determining a binding constant for theformation of the complex. The binding constant is the value obtainedwhen the concentration of the complex is divided by the product of thecomponent concentrations. In general, two compounds are said to “bind,”in the context of the present invention, when the binding constant forcomplex formation exceeds about 10³ L/mol. The binding constant maybedetermined using methods well known in the art.

[0374] Binding agents may be further capable of differentiating betweenpatients with and without a hematological malignancy. Such bindingagents generate a signal indicating the presence of a hematologicalmalignancy in at least about 20% of patients with the disease, and willgenerate a negative signal indicating the absence of the disease in atleast about 90% of individuals without the disease. To determine whethera binding agent satisfies this requirement, biological samples (e.g.,blood, sera, urine and/or tumor biopsies) from patients with and withouta hematological malignancy (as determined using standard clinical tests)may be assayed as described herein for the presence of polypeptides thatbind to the binding agent. It will be apparent that a statisticallysignificant number of samples with and without the disease should beassayed. Each binding agent should satisfy the above criteria; however,those of ordinary skill in the art will recognize that binding agentsmay be used in combination to improve sensitivity.

[0375] Any agent that satisfies the above requirements may be a bindingagent. For example, a binding agent may be a ribosome, with or without apeptide component, an RNA molecule or a polypeptide. In a preferredembodiment, a binding agent is an antibody or an antigen-bindingfragment thereof. Antibodies may be prepared by any of a variety oftechniques known to those of ordinary skill in the art. See, e.g.,Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring HarborLaboratory, 1988. In general, antibodies can be produced by cell culturetechniques, including the generation of monoclonal antibodies asdescribed herein, or via transfection of antibody genes into suitablebacterial or mammalian cell hosts, in order to allow for the productionof recombinant antibodies. In one technique, an immunogen comprising thepolypeptide is initially injected into any of a wide variety of mammals(e.g., mice, rats, rabbits, sheep or goats). In this step, thepolypeptides of this invention may serve as the immunogen withoutmodification. Alternatively, particularly for relatively shortpolypeptides, a superior immune response may be elicited if thepolypeptide is joined to a carrier protein, such as bovine serum albuminor keyhole limpet hemocyanin. The immunogen is injected into the animalhost, preferably according to a predetermined schedule incorporating oneor more booster immunizations, and the animals are bled periodically.Polyclonal antibodies specific for the polypeptide may then be purifiedfrom such antisera by, for example, affinity chromatography using thepolypeptide coupled to a suitable solid support.

[0376] Monoclonal antibodies specific for an antigenic polypeptide ofinterest may be prepared, for example, using the technique of Kohler andMilstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto.Briefly, these methods involve the preparation of immortal cell linescapable of producing antibodies having the desired specificity (i.e.,reactivity with the polypeptide of interest). Such cell lines may beproduced, for example, from spleen cells obtained from an animalimmunized as described above. The spleen cells are then immortalized by,for example, fusion with a myeloma cell fusion partner, preferably onethat is syngeneic with the immunized animal. A variety of fusiontechniques may be employed. For example, the spleen cells and myelomacells may be combined with a nonionic detergent for a few minutes andthen plated at low density on a selective medium that supports thegrowth of hybrid cells, but not myeloma cells. A preferred selectiontechnique uses HAT (hypoxanthine, aminopterin, thymidine) selection.After a sufficient time, usually about 1 to 2 weeks, colonies of hybridsare observed. Single colonies are selected and their culturesupernatants tested for binding activity against the polypeptide.Hybridomas having high reactivity and specificity are preferred.

[0377] Monoclonal antibodies may be isolated from the supernatants ofgrowing hybridoma colonies. In addition, various techniques may beemployed to enhance the yield, such as injection of the hybridoma cellline into the peritoneal cavity of a suitable vertebrate host, such as amouse. Monoclonal antibodies may then be harvested from the ascitesfluid or the blood. Contaminants may be removed from the antibodies byconventional techniques, such as chromatography, gel filtration,precipitation, and extraction. The polypeptides of this invention may beused in the purification process in, for example, an affinitychromatography step.

[0378] Within certain embodiments, the use of antigen-binding fragmentsof antibodies may be preferred. Such fragments include Fab fragments,which may be prepared using standard techniques. Briefly,immunoglobulins may be purified from rabbit serum by affinitychromatography on Protein A bead columns (Harlow and Lane, Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory, 1988) and digested bypapain to yield Fab and Fc fragments. The Fab and Fc fragments may beseparated by affinity chromatography on protein A bead columns.

[0379] Monoclonal antibodies, and fragments thereof, of the presentinvention may be coupled to one or more therapeutic agents, such asradionuclides, differentiation inducers, drugs, toxins, and derivativesthereof. Preferred radionuclides include ⁹⁰Y, ¹²³I, ¹²⁵I, ¹³¹I, ¹⁸⁶Re,¹⁸⁸Re, ²¹¹At, and ²¹² Bi. Preferred drugs include methotrexate, andpyrimidine and purine analogs. Preferred differentiation inducersinclude phorbol esters and butyric acid. Preferred toxins include ricin,abrin, diptheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin,Shigella toxin, and pokeweed antiviral protein. For certain in vivo andex vivo therapies, an antibody or fragment thereof is preferably coupledto a cytotoxic agent, such as a radioactive or chemotherapeutic moiety.

[0380] A therapeutic agent may be coupled (e.g., covalently bonded) to asuitable monoclonal antibody either directly or indirectly (e.g., via alinker group). A direct reaction between an agent and an antibody ispossible when each possesses a substituent capable of reacting with theother. For example, a nucleophilic group, such as an amino or sulfhydrylgroup, on one may be capable of reacting with a carbonyl-containinggroup, such as an anhydride or an acid halide, or with an alkyl groupcontaining a good leaving group (e.g., a halide) on the other.

[0381] Alternatively, it may be desirable to couple a therapeutic agentand an antibody via a linker group. A linker group can function as aspacer to distance an antibody from an agent in order to avoidinterference with binding capabilities. A linker group can also serve toincrease the chemical reactivity of a substituent on an agent or anantibody, and thus increase the coupling efficiency. An increase inchemical reactivity may also facilitate the use of agents, or functionalgroups on agents, which otherwise would not be possible.

[0382] It will be evident to those skilled in the art that a variety ofbifunctional or polyfunctional reagents, both homo- andhetero-functional (such as those described in the catalog of the PierceChemical Co., Rockford, Ill.), may be employed as the linker group.Coupling may be effected, for example, through amino groups, carboxylgroups, sulfhydryl groups or oxidized carbohydrate residues. There arenumerous references describing such methodology, e.g., U.S. Pat. No.4,671,958.

[0383] Where a therapeutic agent is more potent when free from theantibody portion of the immunoconjugates of the present invention, itmay be desirable to use a linker group which is cleavable during or uponinternalization into a cell. A number of different cleavable linkergroups have been described. The mechanisms for the intracellular releaseof an agent from these linker groups include cleavage by reduction of adisulfide bond (e.g., U.S. Pat. No. 4,489,710), by irradiation of aphotolabile bond (e.g., U.S. Pat. No. 4,625,014), by hydrolysis ofderivatized amino acid side chains (e.g., U.S. Pat. No. 4,638,045), byserum complement-mediated hydrolysis (e.g., U.S. Pat. No. 4,671,958),and acid-catalyzed hydrolysis (e.g., U.S. Pat. No. 4,569,789).

[0384] It may be desirable to couple more than one agent to an antibody.In one embodiment, multiple molecules of an agent are coupled to oneantibody molecule. In another embodiment, more than one type of agentmay be coupled to one antibody. Regardless of the particular embodiment,immunoconjugates with more than one agent may be prepared in a varietyof ways. For example, more than one agent may be coupled directly to anantibody molecule, or linkers which provide multiple sites forattachment can be used. Alternatively, a carrier can be used.

[0385] A carrier may bear the agents in a variety of ways, includingcovalent bonding either directly or via a linker group. Suitablecarriers include proteins such as albumins (e.g., U.S. Pat. No.4,507,234), peptides and polysaccharides such as aminodextran (e.g.,U.S. Pat. No. 4,699,784). A carrier may also bear an agent bynoncovalent bonding or by encapsulation, such as within a liposomevesicle (e.g., U.S. Pat. Nos. 4,429,008 and 4,873,088). Carriersspecific for radionuclide agents include radiohalogenated smallmolecules and chelating compounds. For example, U.S. Pat. No. 4,735,792discloses representative radiohalogenated small molecules and theirsynthesis. A radionuclide chelate may be formed from chelating compoundsthat include those containing nitrogen and sulfur atoms as the donoratoms for binding the metal, or metal oxide, radionuclide. For example,U.S. Pat. No. 4,673,562 discloses representative chelating compounds andtheir synthesis.

[0386] A variety of routes of administration for the antibodies andimmunoconjugates may be used. Typically, administration will beintravenous, intramuscular, subcutaneous or in the bed of a resectedtumor. It will be evident that the precise dose of theantibody/immunoconjugate will vary depending upon the antibody used, theantigen density on the tumor, and the rate of clearance of the antibody.

[0387] 4.21 Vaccines

[0388] In certain preferred embodiments of the present invention,vaccines are provided. The vaccines will generally comprise one or morepharmaceutical compositions, such as those discussed above, incombination with an immunostimulant. An immunostimulant may be anysubstance that enhances or potentiates an immune response (antibodyand/or cell-mediated) to an exogenous antigen. Examples ofimmunostimulants include adjuvants, biodegradable microspheres (e.g.,polylactic galactide) and liposomes (into which the compound isincorporated; see e.g., Fullerton, U.S. Pat. No. 4,235,877). Vaccinepreparation is generally described in, for example, M. F. Powell and M.J. Newman, eds., “Vaccine Design (the subunit and adjuvant approach),”Plenum Press (NY, 1995). Pharmaceutical compositions and vaccines withinthe scope of the present invention may also contain other compounds,which may be biologically active or inactive. For example, one or moreimmunogenic portions of other tumor antigens may be present, eitherincorporated into a fusion polypeptide or as a separate compound, withinthe composition or vaccine.

[0389] Illustrative vaccines may contain DNA encoding one or more of thepolypeptides as described above, such that the polypeptide is generatedin situ. As noted above, the DNA may be present within any of a varietyof delivery systems known to those of ordinary skill in the art,including nucleic acid expression systems, bacteria and viral expressionsystems. Numerous gene delivery techniques are well known in the art,such as those described by Rolland, Crit. Rev. Therap. Drug CarrierSystems 15:143-198, 1998, and references cited therein. Appropriatenucleic acid expression systems contain the necessary DNA sequences forexpression in the patient (such as a suitable promoter and terminatingsignal). Bacterial delivery systems involve the administration of abacterium (such as Bacillus-Calmette-Guerrin) that expresses animmunogenic portion of the polypeptide on its cell surface or secretessuch an epitope. In a preferred embodiment, the DNA may be introducedusing a viral expression system (e.g., vaccinia or other pox virus,retrovirus, or adenovirus), which may involve the use of anon-pathogenic (defective), replication competent virus. Suitablesystems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl.Acad. Sci. USA 86:317-321, 1989; Flexner et al., Ann. N.Y. Acad. Sci.569:86-103, 1989; Flexner et al., Vaccine 8:17-21, 1990; U.S. Pat. Nos.4,603,112, 4,769,330, and 5,017,487; WO 89/01973; U.S. Pat. No.4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805; Berkner,Biotechniques 6:616-627, 1988; Rosenfeld et al., Science 252:431-434,1991; Kolls et al., Proc. Natl. Acad. Sci. USA 91:215-219, 1994;Kass-Eisler et al., Proc. Natl. Acad. Sci. USA 90:11498-11502, 1993;Guzman et al., Circulation 88:2838-2848, 1993; and Guzman et al., Cir.Res. 73:1202-1207, 1993. Techniques for incorporating DNA into suchexpression systems are well known to those of ordinary skill in the art.The DNA may also be “naked,” as described, for example, in Ulmer et al.,Science 259:1745-1749, 1993 and reviewed by Cohen, Science259:1691-1692, 1993. The uptake of naked DNA may be increased by coatingthe DNA onto biodegradable beads, which are efficiently transported intothe cells. It will be apparent that a vaccine may comprise both apolynucleotide and a polypeptide component. Such vaccines may providefor an enhanced immune response.

[0390] It will be apparent that a vaccine may contain pharmaceuticallyacceptable salts of the polynucleotides and polypeptides providedherein. Such salts may be prepared from pharmaceutically acceptablenon-toxic bases, including organic bases (e.g., salts of primary,secondary and tertiary amines and basic amino acids) and inorganic bases(e.g., sodium, potassium, lithium, ammonium, calcium and magnesiumsalts).

[0391] While any suitable carrier known to those of ordinary skill inthe art may be employed in the vaccine compositions of this invention,the type of carrier will vary depending on the mode of administration.Compositions of the present invention may be formulated for anyappropriate manner of administration, including for example, topical,oral, nasal, intravenous, intracranial, intraperitoneal, subcutaneous orintramuscular administration. For parenteral administration, such assubcutaneous injection, the carrier preferably comprises water, saline,alcohol, a fat, a wax or a buffer. For oral administration, any of theabove carriers or a solid carrier, such as mannitol, lactose, starch,magnesium stearate, sodium saccharine, talcum, cellulose, glucose,sucrose, and magnesium carbonate, may be employed. Biodegradablemicrospheres (e.g., polylactate polyglycolate) may also be employed ascarriers for the pharmaceutical compositions of this invention. Suitablebiodegradable microspheres are disclosed, for example, in U.S. Pat. Nos.4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763;5,814,344 and 5,942,252. One may also employ a carrier comprising theparticulate-protein complexes described in U.S. Pat. No. 5,928,647,which are capable of inducing a class I-restricted cytotoxic Tlymphocyte responses in a host.

[0392] Such compositions may also comprise buffers (e.g., neutralbuffered saline or phosphate buffered saline), carbohydrates (e.g.,glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptidesor amino acids such as glycine, antioxidants, bacteriostats, chelatingagents such as EDTA or glutathione, adjuvants (e.g., aluminumhydroxide), solutes that render the formulation isotonic, hypotonic orweakly hypertonic with the blood of a recipient, suspending agents,thickening agents and/or preservatives. Alternatively, compositions ofthe present invention may be formulated as a lyophilizate. Compounds mayalso be encapsulated within liposomes using well known technology.

[0393] Any of a variety of immunostimulants may be employed in thevaccines of this invention. For example, an adjuvant may be included.Most adjuvants contain a substance designed to protect the antigen fromrapid catabolism, such as aluminum hydroxide or mineral oil, and astimulator of immune responses, such as lipid A, Bortadella pertussis orMycobacterium tuberculosis derived proteins. Suitable adjuvants arecommercially available as, for example, Freund's Incomplete Adjuvant andComplete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant65 (Merck and Company, Inc., Rahway, N.J.); AS-2 (SmithKline Beecham,Philadelphia, Pa.); aluminum salts such as aluminum hydroxide gel (alum)or aluminum phosphate; salts of calcium, iron or zinc; an insolublesuspension of acylated tyrosine; acylated sugars; cationically oranionically derivatized polysaccharides; polyphosphazenes; biodegradablemicrospheres; monophosphoryl lipid A and quil A. Cytokines, such asGM-CSF or interleukin-2, -7, or -12, may also be used as adjuvants.

[0394] Within the vaccines provided herein, the adjuvant composition ispreferably designed to induce an immune response predominantly of theTh1 type. High levels of Th1-type cytokines (e.g., IFN-γ, TNFα, IL-2 andIL-12) tend to favor the induction of cell mediated immune responses toan administered antigen. In contrast, high levels of Th2-type cytokines(e.g., L-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoralimmune responses. Following application of a vaccine as provided herein,a patient will support an immune response that includes Th1- andTh2-type responses. Within a preferred embodiment, in which a responseis predominantly Th1-type, the level of Th1-type cytokines will increaseto a greater extent than the level of Th2-type cytokines. The levels ofthese cytokines may be readily assessed using standard assays. For areview of the families of cytokines, see Mosmann and Coffman, Ann. Rev.Immunol. 7:145-173, 1989.

[0395] Preferred adjuvants for use in eliciting a predominantly Th1-typeresponse include, for example, a combination of monophosphoryl lipid A,preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPL), togetherwith an aluminum salt. MPL adjuvants are available from CorixaCorporation (Seattle, Wash.; see U.S. Pat. Nos. 4,436,727; 4,877,611;4,866,034 and 4,912,094). CpG-containing oligonucleotides (in which theCpG dinucleotide is unmethylated) also induce a predominantly Th1response. Such oligonucleotides are well known and are described, forexample, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and5,856,462. Immunostimulatory DNA sequences are also described, forexample, by Sato et al., Science 273:352, 1996. Another preferredadjuvant is a saponin, preferably QS21 (Aquila Biopharmaceuticals Inc.,Framingham, Mass.), which may be used alone or in combination with otheradjuvants. For example, an enhanced system involves the combination of amonophosphoryl lipid A and saponin derivative, such as the combinationof QS21 and 3D-MPL as described in WO 94/00153, or a less reactogeniccomposition where the QS21 is quenched with cholesterol, as described inWO 96/33739. Other preferred formulations comprise an oil-in-wateremulsion and tocopherol. A particularly potent adjuvant formulationinvolving QS21, 3D-MPL and tocopherol in an oil-in-water emulsion isdescribed in WO 95/17210.

[0396] Other preferred adjuvants include Montanide ISA 720 (Seppic,France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59(Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4,available from SmithKline Beecham, Rixensart, Belgium), Detox (Corixa,Hamilton, Mont.), RC-529 (Corixa, Hamilton, Mont.) and other aminoalkylglucosaminide 4-phosphates (AGPs), such as those described in pendingU.S. patent application Ser. Nos. 08/853,826 and 09/074,720, thedisclosures of which are incorporated herein by reference in theirentireties.

[0397] Any vaccine provided herein may be prepared using well knownmethods that result in a combination of antigen, immune responseenhancer and a suitable carrier or excipient. The compositions describedherein may be administered as part of a sustained release formulation(i.e., a formulation such as a capsule, sponge or gel (composed ofpolysaccharides, for example) that effects a slow release of compoundfollowing administration). Such formulations may generally be preparedusing well known technology (see, e.g., Coombes et al., Vaccine14:1429-1438, 1996) and administered by, for example, oral, rectal orsubcutaneous implantation, or by implantation at the desired targetsite. Sustained-release formulations may contain a polypeptide,polynucleotide or antibody dispersed in a carrier matrix and/orcontained within a reservoir surrounded by a rate controlling membrane.

[0398] Carriers for use within such formulations are biocompatible, andmay also be biodegradable; preferably the formulation provides arelatively constant level of active component release. Such carriersinclude microparticles of poly(lactide-co-glycolide), polyacrylate,latex, starch, cellulose, dextran and the like. Other delayed-releasecarriers include supramolecular biovectors, which comprise a non-liquidhydrophilic core (e.g., a cross-linked polysaccharide oroligosaccharide) and, optionally, an external layer comprising anamphiphilic compound, such as a phospholipid (see e.g., U.S. Pat. No.5,151,254 and PCT applications WO 94/20078, WO/94/23701 and WO96/06638). The amount of active compound contained within a sustainedrelease formulation depends upon the site of implantation, the rate andexpected duration of release and the nature of the condition to betreated or prevented.

[0399] Any of a variety of delivery vehicles may be employed withinpharmaceutical compositions and vaccines to facilitate production of anantigen-specific immune response that targets tumor cells. Deliveryvehicles include antigen presenting cells (APCs), such as dendriticcells, macrophages, B cells, monocytes and other cells that may beengineered to be efficient APCs. Such cells may, but need not, begenetically modified to increase the capacity for presenting theantigen, to improve activation and/or maintenance of the T cellresponse, to have anti-tumor effects per se and/or to be immunologicallycompatible with the receiver (i.e., matched HLA haplotype). APCs maygenerally be isolated from any of a variety of biological fluids andorgans, including tumor and peritumoral tissues, and may be autologous,allogeneic, syngeneic or xenogeneic cells.

[0400] Certain preferred embodiments of the present invention usedendritic cells or progenitors thereof as antigen-presenting cells.Dendritic cells are highly potent APCs (Banchereau and Steinman, Nature392:245-251, 1998) and have been shown to be effective as aphysiological adjuvant for eliciting prophylactic or therapeuticantitumor immunity (see Timmerman and Levy, Ann. Rev. Med. 50:507-529,1999). In general, dendritic cells may be identified based on theirtypical shape (stellate in situ, with marked cytoplasmic processes(dendrites) visible in vitro), their ability to take up, process andpresent antigens with high efficiency and their ability to activatenaive T cell responses. Dendritic cells may, of course, be engineered toexpress specific cell-surface receptors or ligands that are not commonlyfound on dendritic cells in vivo or ex vivo, and such modified dendriticcells are contemplated by the present invention. As an alternative todendritic cells, secreted vesicles antigen-loaded dendritic cells(called exosomes) may be used within a vaccine (see Zitvogel et al.,Nature Med. 4:594-600, 1998).

[0401] Dendritic cells and progenitors may be obtained from peripheralblood, bone marrow, tumor-infiltrating cells, peritumoraltissues-infiltrating cells, lymph nodes, spleen, skin, umbilical cordblood or any other suitable tissue or fluid. For example, dendriticcells may be differentiated ex vivo by adding a combination of cytokinessuch as GM-CSF, IL-4, IL-13 and/or TNFα to cultures of monocytesharvested from peripheral blood. Alternatively, CD34 positive cellsharvested from peripheral blood, umbilical cord blood or bone marrow maybe differentiated into dendritic cells by adding to the culture mediumcombinations of GM-CSF, IL-3, TNFα, CD40 ligand, LPS, flt3 ligand and/orother compound(s) that induce differentiation, maturation andproliferation of dendritic cells.

[0402] Dendritic cells are conveniently categorized as “immature” and“mature” cells, which allows a simple way to discriminate between twowell characterized phenotypes. However, this nomenclature should not beconstrued to exclude all possible intermediate stages ofdifferentiation. Immature dendritic cells are characterized as APC witha high capacity for antigen uptake and processing, which correlates withthe high expression of Fcγ receptor and mannose receptor. The maturephenotype is typically characterized by a lower expression of thesemarkers, but a high expression of cell surface molecules responsible forT cell activation such as class I and class II MHC, adhesion molecules(e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80,CD86 and 4-1BB).

[0403] APCs may generally be transfected with a polynucleotide encodinga hematological malignancy-related tumor protein (or portion or othervariant thereof) such that the hematological malignancy-related tumorpolypeptide, or an immunogenic portion thereof, is expressed on the cellsurface. Such transfection may take place ex vivo, and a composition orvaccine comprising such transfected cells may then be used fortherapeutic purposes, as described herein. Alternatively, a genedelivery vehicle that targets a dendritic or other antigen presentingcell may be administered to a patient, resulting in transfection thatoccurs in vivo. In vivo and ex vivo transfection of dendritic cells, forexample, may generally be performed using any methods known in the art,such as those described in WO 97/24447, or the gene gun approachdescribed by Mahvi et al., Immunology and cell Biology 75:456-460, 1997.Antigen loading of dendritic cells may be achieved by incubatingdendritic cells or progenitor cells with the hematologicalmalignancy-related tumor polypeptide, DNA (naked or within a plasmidvector) or RNA; or with antigen-expressing recombinant bacterium orviruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors).Prior to loading, the polypeptide may be covalently conjugated to animmunological partner that provides T cell help (e.g., a carriermolecule). Alternatively, a dendritic cell may be pulsed with anon-conjugated immunological partner, separately or in the presence ofthe polypeptide.

[0404] Vaccines and pharmaceutical compositions may be presented inunit-dose or multi-dose containers, such as sealed ampoules or vials.Such containers are preferably hermetically sealed to preserve sterilityof the formulation until use. In general, formulations may be stored assuspensions, solutions or emulsions in oily or aqueous vehicles.Alternatively, a vaccine or pharmaceutical composition may be stored ina freeze-dried condition requiring only the addition of a sterile liquidcarrier immediately prior to use.

[0405] 4.22 Cancer Therapy

[0406] In further aspects of the present invention, the compositionsdescribed herein may be used for immunotherapy of cancer, such ashematological malignancy. Within such methods, pharmaceuticalcompositions and vaccines are typically administered to a patient. Asused herein, a “patient” refers to any warm-blooded animal, preferably ahuman. A patient may or may not be afflicted with cancer. Accordingly,the above pharmaceutical compositions and vaccines may be used toprevent the development of a cancer or to treat a patient afflicted witha cancer. A cancer may be diagnosed using criteria generally accepted inthe art, including the presence of a malignant tumor. Pharmaceuticalcompositions and vaccines may be administered either prior to orfollowing surgical removal of primary tumors and/or treatment such asadministration of radiotherapy or conventional chemotherapeutic drugs.Administration may be by any suitable method, including administrationby intravenous, intraperitoneal, intramuscular, subcutaneous,intranasal, intradermal, anal, vaginal, topical and oral routes.

[0407] Within certain embodiments, immunotherapy may be activeimmunotherapy, in which treatment relies on the in vivo stimulation ofthe endogenous host immune system to react against tumors with theadministration of immune response-modifying agents (such as polypeptidesand polynucleotides as provided herein).

[0408] Within other embodiments, immunotherapy may be passiveimmunotherapy, in which treatment involves the delivery of agents withestablished tumor-immune reactivity (such as effector cells orantibodies) that can directly or indirectly mediate antitumor effectsand does not necessarily depend on an intact host immune system.Examples of effector cells include T cells as discussed above, Tlymphocytes (such as CD8⁺ cytotoxic T lymphocytes and CD4⁺ T-helpertumor-infiltrating lymphocytes), killer cells (such as Natural Killercells and lymphokine-activated killer cells), B cells andantigen-presenting cells (such as dendritic cells and macrophages)expressing a polypeptide provided herein. T cell receptors and antibodyreceptors specific for the polypeptides recited herein may be cloned,expressed and transferred into other vectors or effector cells foradoptive immunotherapy. The polypeptides provided herein may also beused to generate antibodies or anti-idiotypic antibodies (as describedabove and in U.S. Pat. No. 4,918,164) for passive immunotherapy.

[0409] Effector cells may generally be obtained in sufficient quantitiesfor adoptive immunotherapy by growth in vitro, as described herein.Culture conditions for expanding single antigen-specific effector cellsto several billion in number with retention of antigen recognition invivo are well known in the art. Such in vitro culture conditionstypically use intermittent stimulation with antigen, often in thepresence of cytokines (such as IL-2) and non-dividing feeder cells. Asnoted above, immunoreactive polypeptides as provided herein may be usedto rapidly expand antigen-specific T cell cultures in order to generatea sufficient number of cells for immunotherapy. In particular,antigen-presenting cells, such as dendritic, macrophage, monocyte,fibroblast and/or B cells, may be pulsed with immunoreactivepolypeptides or transfected with one or more polynucleotides usingstandard techniques well known in the art. For example,antigen-presenting cells can be transfected with a polynucleotide havinga promoter appropriate for increasing expression in a recombinant virusor other expression system. Cultured effector cells for use in therapymust be able to grow and distribute widely, and to survive long term invivo. Studies have shown that cultured effector cells can be induced togrow in vivo and to survive long term in substantial numbers by repeatedstimulation with antigen supplemented with IL-2 (see, for example,Cheever et al., Immunological Reviews 157:177, 1997).

[0410] Alternatively, a vector expressing a polypeptide recited hereinmay be introduced into antigen presenting cells taken from a patient andclonally propagated ex vivo for transplant back into the same patient.Transfected cells may be reintroduced into the patient using any meansknown in the art, preferably in sterile form by intravenous,intracavitary, intraperitoneal or intratumor administration.

[0411] Routes and frequency of administration of the therapeuticcompositions described herein, as well as dosage, will vary fromindividual to individual, and may be readily established using standardtechniques. In general, the pharmaceutical compositions and vaccines maybe administered by injection (e.g., intracutaneous, intramuscular,intravenous or subcutaneous), intranasally (e.g., by aspiration) ororally. Preferably, between 1 and 10 doses may be administered over a 52week period. Preferably, 6 doses are administered, at intervals of 1month, and booster vaccinations may be given periodically thereafter.Alternate protocols may be appropriate for individual patients. Asuitable dose is an amount of a compound that, when administered asdescribed above, is capable of promoting an anti-tumor immune response,and is at least 10-50% above the basal (i.e., untreated) level. Suchresponse can be monitored by measuring the anti-tumor antibodies in apatient or by vaccine-dependent generation of cytolytic effector cellscapable of killing the patient's tumor cells in vitro. Such vaccinesshould also be capable of causing an immune response that leads to animproved clinical outcome (e.g., more frequent remissions, complete orpartial or longer disease-free survival) in vaccinated patients ascompared to non-vaccinated patients. In general, for pharmaceuticalcompositions and vaccines comprising one or more polypeptides, theamount of each polypeptide present in a dose ranges from about 25 μg to5 mg per kg of host. Suitable dose sizes will vary with the size of thepatient, but will typically range from about 0.1 mL to about 5 mL.

[0412] In general, an appropriate dosage and treatment regimen providesthe active compound(s) in an amount sufficient to provide therapeuticand/or prophylactic benefit. Such a response can be monitored byestablishing an improved clinical outcome (e.g., more frequentremissions, complete or partial, or longer disease-free survival) intreated patients as compared to non-treated patients. Increases inpreexisting immune responses to a hematological malignancy-related tumorprotein generally correlate with an improved clinical outcome. Suchimmune responses may generally be evaluated using standardproliferation, cytotoxicity or cytokine assays, which may be performedusing samples obtained from a patient before and after treatment.

[0413] 4.23 Cancer Detection and Diagnosis

[0414] In general, a cancer may be detected in a patient based on thepresence of one or more hematological malignancy-related tumor proteinsand/or polynucleotides encoding such proteins in a biological sample(for example, blood, sera, sputum urine and/or tumor biopsies) obtainedfrom the patient. In other words, such proteins may be used as markersto indicate the presence or absence of a cancer such as hematologicalmalignancy. In addition, such proteins may be useful for the detectionof other cancers. The binding agents provided herein generally permitdetection of the level of antigen that binds to the agent in thebiological sample. Polynucleotide primers and probes may be used todetect the level of mRNA encoding a tumor protein, which is alsoindicative of the presence or absence of a cancer. In general, ahematological malignancy-related tumor sequence should be present at alevel that is at least three fold higher in tumor tissue than in normaltissue

[0415] There are a variety of assay formats known to those of ordinaryskill in the art for using a binding agent to detect polypeptide markersin a sample. See, e.g., Harlow and Lane, Antibodies: A LaboratoryManual, Cold Spring Harbor Laboratory, 1988. In general, the presence orabsence of a cancer in a patient may be determined by (a) contacting abiological sample obtained from a patient with a binding agent; (b)detecting in the sample a level of polypeptide that binds to the bindingagent; and (c) comparing the level of polypeptide with a predeterminedcut-off value.

[0416] In a preferred embodiment, the assay involves the use of bindingagent immobilized on a solid support to bind to and remove thepolypeptide from the remainder of the sample. The bound polypeptide maythen be detected using a detection reagent that contains a reportergroup and specifically binds to the binding agent/polypeptide complex.Such detection reagents may comprise, for example, a binding agent thatspecifically binds to the polypeptide or an antibody or other agent thatspecifically binds to the binding agent, such as an anti-immunoglobulin,protein G, protein A or a lectin. Alternatively, a competitive assay maybe utilized, in which a polypeptide is labeled with a reporter group andallowed to bind to the immobilized binding agent after incubation of thebinding agent with the sample. The extent to which components of thesample inhibit the binding of the labeled polypeptide to the bindingagent is indicative of the reactivity of the sample with the immobilizedbinding agent. Suitable polypeptides for use within such assays includefull length hematological malignancy-related tumor proteins and portionsthereof to which the binding agent binds, as described above.

[0417] The solid support may be any material known to those of ordinaryskill in the art to which the tumor protein may be attached. Forexample, the solid support may be a test well in a microtiter plate or anitrocellulose or other suitable membrane. Alternatively, the supportmay be a bead or disc, such as glass, fiberglass, latex or a plasticmaterial such as polystyrene or polyvinylchloride. The support may alsobe a magnetic particle or a fiber optic sensor, such as those disclosed,for example, in U.S. Pat. No. 5,359,681. The binding agent may beimmobilized on the solid support using a variety of techniques known tothose of skill in the art, which are amply described in the patent andscientific literature. In the context of the present invention, the term“immobilization” refers to both noncovalent association, such asadsorption, and covalent attachment (which may be a direct linkagebetween the agent and functional groups on the support or may be alinkage by way of a cross-linking agent). Immobilization by adsorptionto a well in a microtiter plate or to a membrane is preferred. In suchcases, adsorption may be achieved by contacting the binding agent, in asuitable buffer, with the solid support for a suitable amount of time.The contact time varies with temperature, but is typically between about1 hour and about 1 day. In general, contacting a well of a plasticmicrotiter plate (such as polystyrene or polyvinylchloride) with anamount of binding agent ranging from about 10 ng to about 10 μg, andpreferably about 100 ng to about 1 μg, is sufficient to immobilize anadequate amount of binding agent.

[0418] Covalent attachment of binding agent to a solid support maygenerally be achieved by first reacting the support with a bifunctionalreagent that will react with both the support and a functional group,such as a hydroxyl or amino group, on the binding agent. For example,the binding agent may be covalently attached to supports having anappropriate polymer coating using benzoquinone or by condensation of analdehyde group on the support with an amine and an active hydrogen onthe binding partner (see, e.g., Pierce Immunotechnology Catalog andHandbook, 1991, at A12-A13).

[0419] In certain embodiments, the assay is a two-antibody sandwichassay. This assay may be performed by first contacting an antibody thathas been immobilized on a solid support, commonly the well of amicrotiter plate, with the sample, such that polypeptides within thesample are allowed to bind to the immobilized antibody. Unbound sampleis then removed from the immobilized polypeptide-antibody complexes anda detection reagent (preferably a second antibody capable of binding toa different site on the polypeptide) containing a reporter group isadded. The amount of detection reagent that remains bound to the solidsupport is then determined using a method appropriate for the specificreporter group.

[0420] More specifically, once the antibody is immobilized on thesupport as described above, the remaining protein binding sites on thesupport are typically blocked. Any suitable blocking agent known tothose of ordinary skill in the art, such as bovine serum albumin orTween 20™ (Sigma Chemical Co., St. Louis, Mo.). The immobilized antibodyis then incubated with the sample, and polypeptide is allowed to bind tothe antibody. The sample may be diluted with a suitable diluent, such asphosphate-buffered saline (PBS) prior to incubation. In general, anappropriate contact time (i.e., incubation time) is a period of timethat is sufficient to detect the presence of polypeptide within a sampleobtained from an individual with hematological malignancy. Preferably,the contact time is sufficient to achieve a level of binding that is atleast about 95% of that achieved at equilibrium between bound andunbound polypeptide. Those of ordinary skill in the art will recognizethat the time necessary to achieve equilibrium may be readily determinedby assaying the level of binding that occurs over a period of time. Atroom temperature, an incubation time of about 30 minutes is generallysufficient.

[0421] Unbound sample may then be removed by washing the solid supportwith an appropriate buffer, such as PBS containing 0.1% Tween 20™. Thesecond antibody, which contains a reporter group, may then be added tothe solid support. Preferred reporter groups include those groupsrecited above.

[0422] The detection reagent is then incubated with the immobilizedantibody-polypeptide complex for an amount of time sufficient to detectthe bound polypeptide. An appropriate amount of time may generally bedetermined by assaying the level of binding that occurs over a period oftime. Unbound detection reagent is then removed and bound detectionreagent is detected using the reporter group. The method employed fordetecting the reporter group depends upon the nature of the reportergroup. For radioactive groups, scintillation counting orautoradiographic methods are generally appropriate. Spectroscopicmethods may be used to detect dyes, luminescent groups and fluorescentgroups. Biotin may be detected using avidin, coupled to a differentreporter group (commonly a radioactive or fluorescent group or anenzyme). Enzyme reporter groups may generally be detected by theaddition of substrate (generally for a specific period of time),followed by spectroscopic or other analysis of the reaction products.

[0423] To determine the presence or absence of a cancer, such ashematological malignancy, the signal detected from the reporter groupthat remains bound to the solid support is generally compared to asignal that corresponds to a predetermined cut-off value. In onepreferred embodiment, the cut-off value for the detection of a cancer isthe average mean signal obtained when the immobilized antibody isincubated with samples from patients without the cancer. In general, asample generating a signal that is three standard deviations above thepredetermined cut-off value is considered positive for the cancer. In analternate preferred embodiment, the cut-off value is determined using aReceiver Operator Curve, according to the method of Sackett et al.,Clinical Epidemiology: A Basic Science for Clinical Medicine, LittleBrown and Co., 1985, p. 106-7. Briefly, in this embodiment, the cut-offvalue may be determined from a plot of pairs of true positive rates(i.e., sensitivity) and false positive rates (100%-specificity) thatcorrespond to each possible cut-off value for the diagnostic testresult. The cut-off value on the plot that is the closest to the upperleft-hand corner (i.e., the value that encloses the largest area) is themost accurate cut-off value, and a sample generating a signal that ishigher than the cut-off value determined by this method may beconsidered positive. Alternatively, the cut-off value may be shifted tothe left along the plot, to minimize the false positive rate, or to theright, to minimize the false negative rate. In general, a samplegenerating a signal that is higher than the cut-off value determined bythis method is considered positive for a cancer.

[0424] In a related embodiment, the assay is performed in a flow-throughor strip test format, wherein the binding agent is immobilized on amembrane, such as nitrocellulose. In the flow-through test, polypeptideswithin the sample bind to the immobilized binding agent as the samplepasses through the membrane. A second, labeled binding agent then bindsto the binding agent-polypeptide complex as a solution containing thesecond binding agent flows through the membrane. The detection of boundsecond binding agent may then be performed as described above. In thestrip test format, one end of the membrane to which binding agent isbound is immersed in a solution containing the sample. The samplemigrates along the membrane through a region containing second bindingagent and to the area of immobilized binding agent. Concentration ofsecond binding agent at the area of immobilized antibody indicates thepresence of a cancer. Typically, the concentration of second bindingagent at that site generates a pattern, such as a line, that can be readvisually. The absence of such a pattern indicates a negative result. Ingeneral, the amount of binding agent immobilized on the membrane isselected to generate a visually discernible pattern when the biologicalsample contains a level of polypeptide that would be sufficient togenerate a positive signal in the two-antibody sandwich assay, in theformat discussed above. Preferred binding agents for use in such assaysare antibodies and antigen-binding fragments thereof. Preferably, theamount of antibody immobilized on the membrane ranges from about 25 ngto about 1 μg, and more preferably from about 50 ng to about 500 ng.Such tests can typically be performed with a very small amount ofbiological sample.

[0425] Of course, numerous other assay protocols exist that are suitablefor use with the tumor proteins or binding agents of the presentinvention. The above descriptions are intended to be exemplary only. Forexample, it will be apparent to those of ordinary skill in the art thatthe above protocols may be readily modified to use hematologicalmalignancy-related tumor polypeptides to detect antibodies that bind tosuch polypeptides in a biological sample. The detection of suchhematological malignancy-related tumor protein specific antibodies maycorrelate with the presence of a cancer.

[0426] A cancer may also, or alternatively, be detected based on thepresence of T cells that specifically react with a hematologicalmalignancy-related tumor protein in a biological sample. Within certainmethods, a biological sample comprising CD4⁺ and/or CD8⁺ T cellsisolated from a patient is incubated with a hematologicalmalignancy-related tumor polypeptide, a polynucleotide encoding such apolypeptide and/or an APC that expresses at least an immunogenic portionof such a polypeptide, and the presence or absence of specificactivation of the T cells is detected. Suitable biological samplesinclude, but are not limited to, isolated T cells. For example, T cellsmay be isolated from a patient by routine techniques (such as byFicoll/Hypaque density gradient centrifugation of peripheral bloodlymphocytes). T cells may be incubated in vitro for 2-9 days (typically4 days) at 37° C. with polypeptide (e.g., 5-25 μg/ml). It may bedesirable to incubate another aliquot of a T cell sample in the absenceof hematological malignancy-related tumor polypeptide to serve as acontrol. For CD4⁺ T cells, activation is preferably detected byevaluating proliferation of the T cells. For CD8⁺ T cells, activation ispreferably detected by evaluating cytolytic activity. A level ofproliferation that is at least two fold greater and/or a level ofcytolytic activity that is at least 20% greater than in disease-freepatients indicates the presence of a cancer in the patient.

[0427] As noted above, a cancer may also, or alternatively, be detectedbased on the level of mRNA encoding a hematological malignancy-relatedtumor protein in a biological sample. For example, at least twooligonucleotide primers may be employed in a polymerase chain reaction(PCR) based assay to amplify a portion of a hematologicalmalignancy-related tumor cDNA derived from a biological sample, whereinat least one of the oligonucleotide primers is specific for (i.e.,hybridizes to) a polynucleotide encoding the hematologicalmalignancy-related tumor protein. The amplified cDNA is then separatedand detected using techniques well known in the art, such as gelelectrophoresis. Similarly, oligonucleotide probes that specificallyhybridize to a polynucleotide encoding a hematologicalmalignancy-related tumor protein may be used in a hybridization assay todetect the presence of polynucleotide encoding the tumor protein in abiological sample.

[0428] To permit hybridization under assay conditions, oligonucleotideprimers and probes should comprise an oligonucleotide sequence that hasat least about 60%, preferably at least about 75% and more preferably atleast about 90%, identity to a portion of a polynucleotide encoding ahematological malignancy-related tumor protein that is at least 10nucleotides, and preferably at least 20 nucleotides, in length.Preferably, oligonucleotide primers and/or probes hybridize to apolynucleotide encoding a polypeptide described herein under moderatelystringent conditions, as defined above. Oligonucleotide primers and/orprobes which may be usefully employed in the diagnostic methodsdescribed herein preferably are at least 10-40 nucleotides in length. Ina preferred embodiment, the oligonucleotide primers comprise at least 10contiguous nucleotides, more preferably at least 15 contiguousnucleotides, of a DNA molecule having a sequence recited in SEQ IDNO:9598-9610. Techniques for both PCR based assays and hybridizationassays are well known in the art (see, for example, Mullis et al., ColdSpring Harbor Symp. Quant. Biol., 51:263, 1987; Erlich ed., PCRTechnology, Stockton Press, NY, 1989).

[0429] One preferred assay employs RT-PCR, in which PCR is applied inconjunction with reverse transcription. Typically, RNA is extracted froma biological sample, such as biopsy tissue, and is reverse transcribedto produce cDNA molecules. PCR amplification using at least one specificprimer generates a cDNA molecule, which may be separated and visualizedusing, for example, gel electrophoresis. Amplification may be performedon biological samples taken from a test patient and from an individualwho is not afflicted with a cancer. The amplification reaction may beperformed on several dilutions of cDNA spanning two orders of magnitude.A two-fold or greater increase in expression in several dilutions of thetest patient sample as compared to the same dilutions of thenon-cancerous sample is typically considered positive.

[0430] In another embodiment, the compositions described herein may beused as markers for the progression of cancer. In this embodiment,assays as described above for the diagnosis of a cancer may be performedover time, and the change in the level of reactive polypeptide(s) orpolynucleotide(s) evaluated. For example, the assays may be performedevery 24-72 hours for a period of 6 months to 1 year, and thereafterperformed as needed. In general, a cancer is progressing in thosepatients in whom the level of polypeptide or polynucleotide detectedincreases over time. In contrast, the cancer is not progressing when thelevel of reactive polypeptide or polynucleotide either remains constantor decreases with time.

[0431] Certain in vivo diagnostic assays may be performed directly on atumor. One such assay involves contacting tumor cells with a bindingagent. The bound binding agent may then be detected directly orindirectly via a reporter group. Such binding agents may also be used inhistological applications. Alternatively, polynucleotide probes may beused within such applications.

[0432] As noted above, to improve sensitivity, multiple hematologicalmalignancy-related tumor protein markers may be assayed within a givensample. It will be apparent that binding agents specific for differentproteins provided herein may be combined within a single assay. Further,multiple primers or probes may be used concurrently. The selection oftumor protein markers may be based on routine experiments to determinecombinations that results in optimal sensitivity. In addition, oralternatively, assays for tumor proteins provided herein may be combinedwith assays for other known tumor antigens.

[0433] 4.24 Preparation of DNA Sequences

[0434] Certain nucleic acid sequences of cDNA molecules encodingportions of hematological malignancy-related antigens were isolated byPCR™-based subtraction. This technique serves to normalizedifferentially expressed cDNAs, facilitating the recovery of raretranscripts, and also has the advantage of permitting enrichment ofcDNAs with small amounts of polyA RNA material and without multiplerounds of hybridization. To obtain antigens overexpressed innon-Hodgkin's lymphomas, two subtractions were performed with a testerlibrary prepared from a pool of three T cell non-Hodgkin's lymphomamRNAs. The two libraries were independently subtracted with differentpools of driver cDNAs. Driver #1 contained cDNA prepared from specificnormal tissues (lymph node, bone marrow, T cells, heart and brain), andthis subtraction generated the library TCS-D1 (T cell non-Hodgkin'slymphoma subtracted library with driver #1). Driver #2 containednon-specific normal tissues (colon, large intestine, lung, pancreas,spinal cord, skeletal muscle, liver, kidney, skin and brain), and thissubtraction generated the library TCS-D2 (T cell non-Hodgkin's lymphomasubtraction library with driver #2). Two other subtractions wereperformed with a tester library prepared from a pool of three B cellnon-Hodgkin's lymphoma mRNAs. The two libraries were independentlysubtracted with different pools of driver cDNAs. Driver #1 containedcDNA prepared from specific normal tissues (lymph node, bone marrow, Bcells, heart and brain), and this subtraction generated the libraryBCNHL/D1 (B cell non-Hodgkin's lymphoma subtracted library with driver#1). Driver #2 contained non-specific normal tissues (brain, lung,pancreas, spinal cord, skeletal muscle, colon, spleen, large intestineand PBMC), and this subtraction generated the library BCNHL/D2 (B cellnon-Hodgkin's lymphoma subtraction library with driver #2).PCR™-amplified pools were generated from the subtracted libraries andclones were sequenced. Hematological malignancy-related antigensequences may be further characterized using any of a variety of wellknown techniques. For example, PCR™ amplified clones may be arrayed ontoglass slides for microarray analysis. To determine tissue distribution,the arrayed clones may be used as targets to be hybridized withdifferent first strand cDNA probes, including lymphoma probes, leukemiaprobes and probes from different normal tissues. Leukemia and lymphomaprobes may be generated from cryopreserved samples obtained at the timeof diagnosis from NHL, Hodgkin's disease, AML, CML, CLL, ALL, MDS andmyeloma patients with poor outcome (patients who failed to achievecomplete remission following conventional chemotherapy or relapsed) orgood outcome (patients who achieved long term remission). To analyzegene expression during hematopoetic differentiation, probes may begenerated from >95% pure fractions of CD34+, CD2+, CD14+, CD15+ andCD19+cells derived from healthy individuals.

[0435] Polynucleotide variants may generally be prepared by any methodknown in the art, including chemical synthesis by, for example, solidphase phosphoramidite chemical synthesis. Modifications in apolynucleotide sequence may also be introduced using standardmutagenesis techniques, such as oligonucleotide-directed site-specificmutagenesis (see Adelman et al., DNA 2:183, 1983). Alternatively, RNAmolecules may be generated by in vitro or in vivo transcription of DNAsequences, provided that the DNA is incorporated into a vector with asuitable RNA polymerase promoter (such as T7 or SP6). Certain portionsmay be used to prepare an encoded polypeptide, as described herein. Inaddition, or alternatively, a portion may be administered to a patientsuch that the encoded polypeptide is generated in vivo (e.g., bytransfecting antigen-presenting cells, such as dendritic cells, with acDNA construct encoding a hematological malignancy-related antigen, andadministering the transfected cells to the patient).

[0436] A portion of a sequence complementary to a coding sequence (i.e.,an antisense polynucleotide) may also be used as a probe or to modulatehematological malignancy-related antigen expression. cDNA constructsthat can be transcribed into antisense RNA may also be introduced intocells or tissues to facilitate the production of antisense RNA. Anantisense polynucleotide may be used, as described herein, to inhibitexpression of a hematological malignancy-related antigen. Antisensetechnology can be used to control gene expression through triple-helixformation, which compromises the ability of the double helix to opensufficiently for the binding of polymerases, transcription factors orregulatory molecules (see Gee et al., In Huber and Carr, Molecular andImmunologic Approaches, Futura Publishing Co. (Mt. Kisco, N.Y.; 1994)).Alternatively, an antisense molecule may be designed to hybridize with acontrol region of a gene (e.g., promoter, enhancer or transcriptioninitiation site), and block transcription of the gene; or to blocktranslation by inhibiting binding of a transcript to ribosomes.

[0437] A portion of a coding sequence or of a complementary sequence mayalso be designed as a probe or primer to detect gene expression. Probesmay be labeled with a variety of reporter groups, such as radionuclidesand enzymes, and are preferably at least 10 nucleotides in length, morepreferably at least 20 nucleotides in length and still more preferablyat least 30 nucleotides in length. Primers, as noted above, arepreferably 22-30 nucleotides in length.

[0438] Any polynucleotide may be further modified to increase stabilityin vivo. Possible modifications include, but are not limited to, theaddition of flanking sequences at the 5′ and/or 3′ ends; the use ofphosphorothioate or 2′ O-methyl rather than phosphodiesterase linkagesin the backbone; and/or the inclusion of nontraditional bases such asinosine, queosine and wybutosine, as well as acetyl- methyl-, thio- andother modified forms of adenine, cytidine, guanine, thymine and uridine.

[0439] Hematological malignancy-related antigen polynucleotides may bejoined to a variety of other nucleotide sequences using establishedrecombinant DNA techniques. For example, a polynucleotide may be clonedinto any of a variety of cloning vectors, including plasmids, phagemids,lambda phage derivatives and cosmids. Vectors of particular interestinclude expression vectors, replication vectors, probe generationvectors and sequencing vectors. In general, a vector will contain anorigin of replication functional in at least one organism, convenientrestriction endonuclease sites and one or more selectable markers. Otherelements will depend upon the desired use, and will be apparent to thoseof ordinary skill in the art.

[0440] Within certain embodiments, polynucleotides may be formulated soas to permit entry into a cell of a mammal, and expression therein. Suchformulations are particularly useful for therapeutic purposes, asdescribed below. Those of ordinary skill in the art will appreciate thatthere are many ways to achieve expression of a polynucleotide in atarget cell, and any suitable method may be employed. For example, apolynucleotide may be incorporated into a viral vector such as, but notlimited to, adenovirus, adeno-associated virus, retrovirus, or vacciniaor other pox virus (e.g., avian pox virus). Techniques for incorporatingDNA into such vectors are well known to those of ordinary skill in theart. A retroviral vector may additionally transfer or incorporate a genefor a selectable marker (to aid in the identification or selection oftransduced cells) and/or a targeting moiety, such as a gene that encodesa ligand for a receptor on a specific target cell, to render the vectortarget specific. Targeting may also be accomplished using an antibody,by methods known to those of ordinary skill in the art.

[0441] Other formulations for therapeutic purposes include colloidaldispersion systems, such as macromolecule complexes, nanocapsules,microspheres, beads, and lipid-based systems including oil-in-wateremulsions, micelles, mixed micelles, and liposomes. A preferredcolloidal system for use as a delivery vehicle in vitro and in vivo is aliposome (i.e., an artificial membrane vesicle). The preparation and useof such systems is well known in the art.

[0442] 4.25 Therapeutic Methods

[0443] In further aspects of the present invention, the compositionsdescribed herein may be used for immunotherapy of hematologicalmalignancies including adult and pediatric AML, CML, ALL, CLL,myelodysplastic syndromes (MDS), myeloproliferative syndromes (MPS),secondary leukemia, multiple myeloma, Hodgkin's lymphoma andNon-Hodgkin's lymphomas. In addition, compositions described herein maybe used for therapy of diseases associated with an autoimmune responseagainst hematopoetic precursor cells, such as severe aplastic anemia.

[0444] Immunotherapy may be performed using any of a variety oftechniques, in which compounds or cells provided herein function toremove hematological malignancy-related antigen-expressing cells from apatient. Such removal may take place as a result of enhancing orinducing an immune response in a patient specific for hematologicalmalignancy-related antigen or a cell expressing hematologicalmalignancy-related antigen. Alternatively, hematologicalmalignancy-related antigen-expressing cells may be removed ex vivo(e.g., by treatment of autologous bone marrow, peripheral blood or afraction of bone marrow or peripheral blood). Fractions of bone marrowor peripheral blood may be obtained using any standard technique in theart.

[0445] Within such methods, pharmaceutical compositions and vaccines aretypically administered to a patient. As used herein, a “patient” refersto any warm-blooded animal, preferably a human. A patient may or may notbe afflicted with a hematological malignancy. Accordingly, the abovepharmaceutical compositions and vaccines may be used to prevent thedevelopment of a malignancy or to treat a patient afflicted with amalignancy. A hematological malignancy may be diagnosed using criteriagenerally accepted in the art. Pharmaceutical compositions and vaccinesmay be administered either prior to or following surgical removal ofprimary tumors and/or treatment such as administration of radiotherapyor conventional chemotherapeutic drugs, or bone marrow transplantation(autologous, allogeneic or syngeneic).

[0446] Within certain embodiments, immunotherapy may be activeimmunotherapy, in which treatment relies on the in vivo stimulation ofthe endogenous host immune system to react against tumors with theadministration of immune response-modifying agents (such as polypeptidesand polynucleotides as provided herein).

[0447] Within other embodiments, immunotherapy may be passiveimmunotherapy, in which treatment involves the delivery of agents withestablished tumor-immune reactivity (such as effector cells orantibodies) that can directly or indirectly mediate antitumor effectsand does not necessarily depend on an intact host immune system.Examples of effector cells include T cells as discussed above, Tlymphocytes (such as CD8⁺ cytotoxic T lymphocytes and CD4⁺ T-helpertumor-infiltrating lymphocytes), killer cells (such as Natural Killercells and lymphokine-activated killer cells), B cells andantigen-presenting cells (such as dendritic cells and macrophages)expressing a polypeptide provided herein. T cell receptors and antibodyreceptors specific for the polypeptides recited herein may be cloned,expressed and transferred into other vectors or effector cells foradoptive immunotherapy. The polypeptides provided herein may also beused to generate antibodies or anti-idiotypic antibodies (as describedabove and in U.S. Pat. No. 4,918,164) for passive immunotherapy.

[0448] Effector cells may generally be obtained in sufficient quantitiesfor adoptive immunotherapy by growth in vitro, as described herein.Culture conditions for expanding single antigen-specific effector cellsto several billion in number with retention of antigen recognition invivo are well known in the art. Such in vitro culture conditionstypically use intermittent stimulation with antigen, often in thepresence of cytokines (such as IL-2) and non-dividing feeder cells. Asnoted above, immunoreactive polypeptides as provided herein may be usedto rapidly expand antigen-specific T cell cultures in order to generatea sufficient number of cells for immunotherapy. In particular,antigen-presenting cells, such as dendritic, macrophage or B cells, maybe pulsed with immunoreactive polypeptides or transfected with one ormore polynucleotides using standard techniques well known in the art.For example, antigen-presenting cells can be transfected with apolynucleotide having a promoter appropriate for increasing expressionin a recombinant virus or other expression system. Cultured effectorcells for use in therapy must be able to grow and distribute widely, andto survive long term in vivo. Studies have shown that cultured effectorcells can be induced to grow in vivo and to survive long term insubstantial numbers by repeated stimulation with antigen supplementedwith IL-2 (see, for example, Cheever et al., Immunological Reviews157:177, 1997).

[0449] Alternatively, a vector expressing a polypeptide recited hereinmay be introduced into antigen presenting cells taken from a patient andclonally propagated ex vivo for transplant back into the same patient.Transfected cells may be reintroduced into the patient using any meansknown in the art, preferably in sterile form by intravenous,intracavitary, intraperitoneal or intratumor administration.

[0450] The compositions provided herein may be used alone or incombination with conventional therapeutic regimens such as surgery,irradiation, chemotherapy and/or bone marrow transplantation(autologous, syngeneic, allogeneic or unrelated). As discussed ingreater detail below, binding agents and T cells as provided herein maybe used for purging of autologous stem cells. Such purging may bebeneficial prior to, for example, bone marrow transplantation ortransfusion of blood or components thereof. Binding agents, T cells,antigen presenting cells (APC) and compositions provided herein mayfurther be used for expanding and stimulating (or priming) autologous,allogeneic, syngeneic or unrelated hematological malignancy-relatedantigen-specific T-cells in vitro and/or in vivo. Such hematologicalmalignancy-related antigen-specific T cells may be used, for example,within donor lymphocyte infusions.

[0451] Routes and frequency of administration of the therapeuticcompositions described herein, as well as dosage, will vary fromindividual to individual, and may be readily established using standardtechniques. In general, the pharmaceutical compositions and vaccines maybe administered by injection (e.g., intracutaneous, intramuscular,intravenous or subcutaneous), intranasally (e.g., by aspiration) ororally. Preferably, between 1 and 10 doses may be administered over a 52week period. Preferably, 6 doses are administered, at intervals of 1month, and booster vaccinations may be given periodically thereafter.Alternate protocols may be appropriate for individual patients. Asuitable dose is an amount of a compound that, when administered asdescribed above, is capable of promoting an anti-tumor immune response,and is at least 10-50% above the basal (i.e., untreated) level. Suchresponse can be monitored by measuring the anti-tumor antibodies in apatient or by vaccine-dependent generation of cytolytic effector cellscapable of killing the patient's tumor cells in vitro. Such vaccinesshould also be capable of causing an immune response that leads to animproved clinical outcome (e.g., more frequent remissions, complete orpartial or longer disease-free survival) in vaccinated patients ascompared to non-vaccinated patients. In general, for pharmaceuticalcompositions and vaccines comprising one or more polypeptides, theamount of each polypeptide present in a dose ranges from about 100 μg to5 mg per kg of host. Suitable dose sizes will vary with the size of thepatient, but will typically range from about 0.1 mL to about 5 mL.

[0452] In general, an appropriate dosage and treatment regimen providesthe active compound(s) in an amount sufficient to provide therapeuticand/or prophylactic benefit. Such a response can be monitored byestablishing an improved clinical outcome (e.g., more frequentremissions, complete or partial, or longer disease-free survival) intreated patients as compared to non-treated patients. Increases inpreexisting immune responses to a hematological malignancy-relatedantigen generally correlate with an improved clinical outcome. Suchimmune responses may generally be evaluated using standardproliferation, cytotoxicity or cytokine assays, which may be performedusing samples obtained from a patient before and after treatment.

[0453] Within further aspects, methods for inhibiting the development ofa malignant disease associated with hematological malignancy-relatedantigen expression involve the administration of autologous T cells thathave been activated in response to a hematological malignancy-relatedantigen polypeptide or hematological malignancy-relatedantigen-expressing APC, as described above. Such T cells may be CD4⁺and/or CD8⁺, and may be proliferated as described above. The T cells maybe administered to the individual in an amount effective to inhibit thedevelopment of a malignant disease. Typically, about 1×10⁹ to 1×10¹¹ Tcells/M² are administered intravenously, intracavitary or in the bed ofa resected tumor. It will be evident to those skilled in the art thatthe number of cells and the frequency of administration will bedependent upon the response of the patient.

[0454] Within certain embodiments, T cells may be stimulated prior to anautologous bone marrow transplantation. Such stimulation may take placein vivo or in vitro. For in vitro stimulation, bone marrow and/orperipheral blood (or a fraction of bone marrow or peripheral blood)obtained from a patient may be contacted with a hematologicalmalignancy-related antigen polypeptide, a polynucleotide encoding ahematological malignancy-related antigen polypeptide and/or an APC thatexpresses a hematological malignancy-related antigen polypeptide underconditions and for a time sufficient to permit the stimulation of Tcells as described above. Bone marrow, peripheral blood stem cellsand/or hematological malignancy-related antigen-specific T cells maythen be administered to a patient using standard techniques.

[0455] Within related embodiments, T cells of a related or unrelateddonor may be stimulated prior to a syngeneic or allogeneic (related orunrelated) bone marrow transplantation. Such stimulation may take placein vivo or in vitro. For in vitro stimulation, bone marrow and/orperipheral blood (or a fraction of bone marrow or peripheral blood)obtained from a related or unrelated donor may be contacted with ahematological malignancy-related antigen polypeptide, hematologicalmalignancy-related antigen polynucleotide and/or APC that expresses ahematological malignancy-related antigen polypeptide under conditionsand for a time sufficient to permit the stimulation of T cells asdescribed above. Bone marrow, peripheral blood stem cells and/orhematological malignancy-related antigen-specific T cells may then beadministered to a patient using standard techniques.

[0456] Within other embodiments, hematological malignancy-relatedantigen-specific T cells, antibodies or antigen-binding fragmentsthereof as described herein may be used to remove cells expressinghematological malignancy-related antigen from a biological sample, suchas autologous bone marrow, peripheral blood or a fraction of bone marrowor peripheral blood (e.g., CD34⁺ enriched peripheral blood (PB) prior toadministration to a patient). Such methods may be performed bycontacting the biological sample with such T cells, antibodies orantibody fragments under conditions and for a time sufficient to permitthe reduction of hematological malignancy-related antigen expressingcells to less than 10%, preferably less than 5% and more preferably lessthan 1%, of the total number of myeloid or lymphatic cells in the bonemarrow or peripheral blood. Such contact may be achieved, for example,using a column to which antibodies are attached using standardtechniques. Antigen-expressing cells are retained on the column. Theextent to which such cells have been removed may be readily determinedby standard methods such as, for example, qualitative and quantitativePCR analysis, morphology, immunohistochemistry and FACS analysis. Bonemarrow or PB (or a fraction thereof) may then be administered to apatient using standard techniques.

[0457] 4.26 Diagnostic Methods

[0458] In general, a hematological malignancy may be detected in apatient based on the presence of hematological malignancy-relatedantigen and/or polynucleotide in a biological sample (such as blood,sera, urine and/or tumor biopsies) obtained from the patient. In otherwords, hematological malignancy-related antigens may be used as a markerto indicate the presence or absence of such a malignancy. The bindingagents provided herein generally permit detection of the level ofantigen that binds to the agent in the biological sample. Polynucleotideprimers and probes may be used to detect the level of mRNA encodinghematological malignancy-related antigen, which is also indicative ofthe presence or absence of a hematological malignancy. In general,hematological malignancy-related antigen should be present at a levelthat is at least three fold higher in a sample obtained from a patientafflicted with a hematological malignancy than in the sample obtainedfrom an individual not so afflicted.

[0459] There are a variety of assay formats known to those of ordinaryskill in the art for using a binding agent to detect polypeptide markersin a sample. See, e.g., Harlow and Lane, Antibodies: A LaboratoryManual, Cold Spring Harbor Laboratory, 1988. In general, the presence orabsence of a hematological malignancy in a patient may be determined by(a) contacting a biological sample obtained from a patient with abinding agent; (b) detecting in the sample a level of polypeptide thatbinds to the binding agent; and (c) comparing the level of polypeptidewith a predetermined cut-off value.

[0460] In a preferred embodiment, the assay involves the use of bindingagent immobilized on a solid support to bind to and remove thepolypeptide from the remainder of the sample. The bound polypeptide maythen be detected using a detection reagent that contains a reportergroup and specifically binds to the binding agent/polypeptide complex.Such detection reagents may comprise, for example, a binding agent thatspecifically binds to the polypeptide or an antibody or other agent thatspecifically binds to the binding agent, such as an anti-immunoglobulin,protein G, protein A or a lectin. Alternatively, a competitive assay maybe utilized, in which a polypeptide is labeled with a reporter group andallowed to bind to the immobilized binding agent after incubation of thebinding agent with the sample. The extent to which components of thesample inhibit the binding of the labeled polypeptide to the bindingagent is indicative of the reactivity of the sample with the immobilizedbinding agent. Suitable polypeptides for use within such assays includefull length hematological malignancy-related antigens and portionsthereof to which the binding agent binds, as described above.

[0461] The solid support may be any material known to those of ordinaryskill in the art to which the hematological malignancy-related antigenpolypeptide may be attached. For example, the solid support may be atest well in a microtiter plate or a nitrocellulose or other suitablemembrane. Alternatively, the support may be a bead or disc, such asglass, fiberglass, latex or a plastic material such as polystyrene orpolyvinylchloride. The support may also be a magnetic particle or afiber optic sensor, such as those disclosed, for example, in U.S. Pat.No. 5,359,681. The binding agent may be immobilized on the solid supportusing a variety of techniques known to those of skill in the art, whichare amply described in the patent and scientific literature. In thecontext of the present invention, the term “immobilization” refers toboth noncovalent association, such as adsorption, and covalentattachment (which may be a direct linkage between the agent andfunctional groups on the support or may be a linkage by way of across-linking agent). Immobilization by adsorption to a well in amicrotiter plate or to a membrane is preferred. In such cases,adsorption may be achieved by contacting the binding agent, in asuitable buffer, with the solid support for a suitable amount of time.The contact time varies with temperature, but is typically between about1 hour and about 1 day. In general, contacting a well of a plasticmicrotiter plate (such as polystyrene or polyvinylchloride) with anamount of binding agent ranging from about 10 ng to about 10 μg, andpreferably about 100 ng to about 1 μg, is sufficient to immobilize anadequate amount of binding agent.

[0462] Covalent attachment of binding agent to a solid support maygenerally be achieved by first reacting the support with a bifunctionalreagent that will react with both the support and a functional group,such as a hydroxyl or amino group, on the binding agent. For example,the binding agent may be covalently attached to supports having anappropriate polymer coating using benzoquinone or by condensation of analdehyde group on the support with an amine and an active hydrogen onthe binding partner (see, e.g., Pierce Immunotechnology Catalog andHandbook, 1991, at A12-A13).

[0463] In certain embodiments, the assay is a two-antibody sandwichassay. This assay may be performed by first contacting an antibody thathas been immobilized on a solid support, commonly the well of amicrotiter plate, with the sample, such that polypeptides within thesample are allowed to bind to the immobilized antibody. Unbound sampleis then removed from the immobilized polypeptide-antibody complexes anda detection reagent (preferably a second antibody capable of binding toa different site on the polypeptide) containing a reporter group isadded. The amount of detection reagent that remains bound to the solidsupport is then determined using a method appropriate for the specificreporter group.

[0464] More specifically, once the antibody is immobilized on thesupport as described above, the remaining protein binding sites on thesupport are typically blocked. Any suitable blocking agent known tothose of ordinary skill in the art, such as bovine serum albumin orTween 20™ (Sigma Chemical Co., St. Louis, Mo.). The immobilized antibodyis then incubated with the sample, and polypeptide is allowed to bind tothe antibody. The sample may be diluted with a suitable diluent, such asphosphate-buffered saline (PBS) prior to incubation. In general, anappropriate contact time (i.e., incubation time) is a period of timethat is sufficient to detect the presence of polypeptide within a sampleobtained from an individual with a hematological malignancy. Preferably,the contact time is sufficient to achieve a level of binding that is atleast about 95% of that achieved at equilibrium between bound andunbound polypeptide. Those of ordinary skill in the art will recognizethat the time necessary to achieve equilibrium may be readily determinedby assaying the level of binding that occurs over a period of time. Atroom temperature, an incubation time of about 30 minutes is generallysufficient.

[0465] Unbound sample may then be removed by washing the solid supportwith an appropriate buffer, such as PBS containing 0.1% Tween 20™. Thesecond antibody, which contains a reporter group, may then be added tothe solid support. Preferred reporter groups include those groupsrecited above.

[0466] The detection reagent is then incubated with the immobilizedantibody-polypeptide complex for an amount of time sufficient to detectthe bound polypeptide. An appropriate amount of time may generally bedetermined by assaying the level of binding that occurs over a period oftime. Unbound detection reagent is then removed and bound detectionreagent is detected using the reporter group. The method employed fordetecting the reporter group depends upon the nature of the reportergroup. For radioactive groups, scintillation counting orautoradiographic methods are generally appropriate. Spectroscopicmethods may be used to detect dyes, luminescent groups and fluorescentgroups. Biotin may be detected using avidin, coupled to a differentreporter group (commonly a radioactive or fluorescent group or anenzyme). Enzyme reporter groups may generally be detected by theaddition of substrate (generally for a specific period of time),followed by spectroscopic or other analysis of the reaction products.

[0467] To determine the presence or absence of a hematologicalmalignancy, the signal detected from the reporter group that remainsbound to the solid support is generally compared to a signal thatcorresponds to a predetermined cut-off value. In one preferredembodiment, the cut-off value for the detection of a hematologicalmalignancy is the average mean signal obtained when the immobilizedantibody is incubated with samples from patients without the malignancy.In general, a sample generating a signal that is three standarddeviations above the predetermined cut-off value is considered positivefor the malignancy. In an alternate preferred embodiment, the cut-offvalue is determined using a Receiver Operator Curve, according to themethod of Sackett et al., Clinical Epidemiology: A Basic Science forClinical Medicine, Little Brown and Co., 1985, p. 106-7. Briefly, inthis embodiment, the cut-off value may be determined from a plot ofpairs of true positive rates (i.e., sensitivity) and false positiverates (100%-specificity) that correspond to each possible cut-off valuefor the diagnostic test result. The cut-off value on the plot that isthe closest to the upper left-hand corner (i.e., the value that enclosesthe largest area) is the most accurate cut-off value, and a samplegenerating a signal that is higher than the cut-off value determined bythis method may be considered positive. Alternatively, the cut-off valuemay be shifted to the left along the plot, to minimize the falsepositive rate, or to the right, to minimize the false negative rate. Ingeneral, a sample generating a signal that is higher than the cut-offvalue determined by this method is considered positive for a malignancy.

[0468] In a related embodiment, the assay is performed in a flow-throughor strip test format, wherein the binding agent is immobilized on amembrane, such as nitrocellulose. In the flow-through test, polypeptideswithin the sample bind to the immobilized binding agent as the samplepasses through the membrane. A second, labeled binding agent then bindsto the binding agent-polypeptide complex as a solution containing thesecond binding agent flows through the membrane. The detection of boundsecond binding agent may then be performed as described above. In thestrip test format, one end of the membrane to which binding agent isbound is immersed in a solution containing the sample. The samplemigrates along the membrane through a region containing second bindingagent and to the area of immobilized binding agent. Concentration ofsecond binding agent at the area of immobilized antibody indicates thepresence of a hematological malignancy. Typically, the concentration ofsecond binding agent at that site generates a pattern, such as a line,that can be read visually. The absence of such a pattern indicates anegative result. In general, the amount of binding agent immobilized onthe membrane is selected to generate a visually discernible pattern whenthe biological sample contains a level of polypeptide that would besufficient to generate a positive signal in the two-antibody sandwichassay, in the format discussed above. Preferred binding agents for usein such assays are antibodies and antigen-binding fragments thereof.Preferably, the amount of antibody immobilized on the membrane rangesfrom about 25 ng to about 1 μg, and more preferably from about 50 ng toabout 500 ng. Such tests can typically be performed with a very smallamount of biological sample.

[0469] Of course, numerous other assay protocols exist that are suitablefor use with the hematological malignancy-related antigen sequences orbinding agents of the present invention. The above descriptions areintended to be exemplary only. For example, it will be apparent to thoseof ordinary skill in the art that the above protocols may be readilymodified to use hematological malignancy-related antigen polypeptides todetect antibodies that bind to such polypeptides in a biological sample.The detection of hematological malignancy-related antigen-specificantibodies may correlate with the presence of a hematological.

[0470] A malignancy may also, or alternatively, be detected based on thepresence of T cells that specifically react with hematologicalmalignancy-related antigen in a biological sample. Within certainmethods, a biological sample comprising CD4⁺ and/or CD8⁺ T cellsisolated from a patient is incubated with a hematologicalmalignancy-related antigen polypeptide, a polynucleotide encoding such apolypeptide and/or an APC that expresses such a polypeptide, and thepresence or absence of specific activation of the T cells is detected.Suitable biological samples include, but are not limited to, isolated Tcells. For example, T cells may be isolated from a patient by routinetechniques (such as by Ficoll/Hypaque density gradient centrifugation ofperipheral blood lymphocytes). T cells may be incubated in vitro for 2-9days (typically 4 days) at 37° C. with Mtb-81 or Mtb-67.2 polypeptide(e.g., 5-25 μg/ml). It may be desirable to incubate another aliquot of aT cell sample in the absence of hematological malignancy-related antigenpolypeptide to serve as a control. For CD4⁺ T cells, activation ispreferably detected by evaluating proliferation of the T cells. For CD8⁺T cells, activation is preferably detected by evaluating cytolyticactivity. A level of proliferation that is at least two fold greaterand/or a level of cytolytic activity that is at least 20% greater thanin disease-free patients indicates the presence of a hematologicalmalignancy in the patient.

[0471] As noted above, a hematological malignancy may also, oralternatively, be detected based on the level of mRNA encodinghematological malignancy-related antigen in a biological sample. Forexample, at least two oligonucleotide primers may be employed in apolymerase chain reaction (PCR) based assay to amplify a portion ofhematological malignancy-related antigen cDNA derived from a biologicalsample, wherein at least one of the oligonucleotide primers is specificfor (i.e., hybridizes to) a polynucleotide encoding the hematologicalmalignancy-related antigen protein. The amplified cDNA is then separatedand detected using techniques well known in the art, such as gelelectrophoresis. Similarly, oligonucleotide probes that specificallyhybridize to a polynucleotide encoding hematological malignancy-relatedantigen may be used in a hybridization assay to detect the presence ofpolynucleotide encoding hematological malignancy-related antigen in abiological sample.

[0472] To permit hybridization under assay conditions, oligonucleotideprimers and probes should comprise an oligonucleotide sequence that hasat least about 60%, preferably at least about 75% and more preferably atleast about 90%, identity to a portion of a polynucleotide encodinghematological malignancy-related antigen that is at least 10nucleotides, and preferably at least 20 nucleotides, in length.Preferably, oligonucleotide primers and/or probes hybridize to apolynucleotide encoding a polypeptide described herein under moderatelystringent conditions, as defined above. Oligonucleotide primers and/orprobes which may be usefully employed in the diagnostic methodsdescribed herein preferably are at least 10-40 nucleotides in length.Techniques for both PCR based assays and hybridization assays are wellknown in the art (see, for example, Mullis et al., Cold Spring HarborSymp. Quant. Biol., 51:263, 1987; Erlich ed., PCR Technology, StocktonPress, NY, 1989).

[0473] One preferred assay employs RT-PCR, in which PCR is applied inconjunction with reverse transcription. Typically, RNA is extracted froma biological sample such as a biopsy tissue and is reverse transcribedto produce cDNA molecules. PCR amplification using at least one specificprimer generates a cDNA molecule, which may be separated and visualizedusing, for example, gel electrophoresis. Amplification may be performedon biological samples taken from a test patient and from an individualwho is not afflicted with a hematological malignancy. The amplificationreaction may be performed on several dilutions of cDNA spanning twoorders of magnitude. A two-fold or greater increase in expression inseveral dilutions of the test patient sample as compared to the samedilutions of the sample from a normal individual is typically consideredpositive.

[0474] In preferred embodiments, such assays may be performed usingsamples enriched for cells expressing the hematologicalmalignancy-related antigen(s) of interest. Such enrichment may beachieved, for example, using a binding agent as provided herein toremove the cells from the remainder of the biological sample. Theremoved cells may then be assayed as described above for biologicalsamples.

[0475] In further embodiments, hematological malignancy-related antigensmay be used as markers for monitoring disease progression or theresponse to therapy of a hematological malignancy. In this embodiment,assays as described above for the diagnosis of a hematologicalmalignancy may be performed over time, and the change in the level ofreactive polypeptide(s) evaluated. For example, the assays may beperformed every 24-72 hours for a period of 6 months to 1 year, andthereafter performed as needed. In general, a malignancy is progressingin those patients in whom the level of polypeptide detected by thebinding agent increases over time. In contrast, the malignancy is notprogressing when the level of reactive polypeptide either remainsconstant or decreases with time.

[0476] Certain in vivo diagnostic assays may be performed directly on atumor. One such assay involves contacting tumor cells with a bindingagent. The bound binding agent may then be detected directly orindirectly via a reporter group. Such binding agents may also be used inhistological applications. Alternatively, polynucleotide probes may beused within such applications.

[0477] As noted above, to improve sensitivity, multiple markers may beassayed within a given sample. It will be apparent that binding agentsspecific for different proteins provided herein may be combined within asingle assay. Further, multiple primers or probes may be usedconcurrently. The selection of markers may be based on routineexperiments to determine combinations that results in optimalsensitivity.

[0478] Further diagnostic applications include the detection ofextramedullary disease (e.g., cerebral infiltration of blasts inleukemias). Within such methods, a binding agent may be coupled to atracer substance, and the diagnosis is performed in vivo using wellknown techniques. Coupled binding agent may be administered as describedabove, and extramedullary disease may be detected based on assaying thepresence of tracer substance. Alternatively, a tracer substance may beassociated with a T cell specific for hematological malignancy-relatedantigen, permitting detection of extramedullary disease based on assaysto detect the location of the tracer substance.

[0479] 4.27 Exemplary Definitions

[0480] In accordance with the present invention, nucleic acid sequencesinclude, but are not limited to, DNAs (including and not limited togenomic or extragenomic DNAs), genes, peptide nucleic acids (PNAs) RNAs(including, but not limited to, rRNAs, mRNAs and tRNAs), nucleosides,and suitable nucleic acid segments either obtained from native sources,chemically synthesized, modified, or otherwise prepared in whole or inpart by the hand of man.

[0481] Unless defined otherwise, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Although any methodsand compositions similar or equivalent to those described herein can beused in the practice or testing of the present invention, the preferredmethods and compositions are described herein. For purposes of thepresent invention, the following terms are defined below:

[0482] A, an: In accordance with long standing patent law convention,the words “a” and “an” when used in this application, including theclaims, denotes “one or more”.

[0483] Expression: The combination of intracellular processes, includingtranscription and translation undergone by a polynucleotide such as astructural gene to synthesize the encoded peptide or polypeptide.

[0484] Promoter: a term used to generally describe the region or regionsof a nucleic acid sequence that regulates transcription.

[0485] Regulatory Element: a term used to generally describe the regionor regions of a nucleic acid sequence that regulates transcription.

[0486] Structural gene: A gene or sequence region that is expressed toproduce an encoded peptide or polypeptide.

[0487] Transformation: A process of introducing an exogenouspolynucleotide sequence (e.g., a vector, a recombinant DNA or RNAmolecule) into a host cell or protoplast in which that exogenous nucleicacid segment is incorporated into at least a first chromosome or iscapable of autonomous replication within the transformed host cell.Transfection, electroporation, and naked nucleic acid uptake allrepresent examples of techniques used to transform a host cell with oneor more polynucleotides.

[0488] Transformed cell: A host cell whose nucleic acid complement hasbeen altered by the introduction of one or more exogenouspolynucleotides into that cell.

[0489] Transgenic cell: Any cell derived or regenerated from atransformed cell or derived from a transgenic cell, or from the progenyor offspring of any generation of such a transformed host cell.

[0490] Transgenic animal: An animal or a progeny or an offspring of anygeneration thereof that is derived from a transformed animal cell,wherein the animal's DNA contains an introduced exogenous nucleic acidmolecule not originally present in a native, wild type, non-transgenicanimal of the same species. The terms “transgenic animal” and“transformed animal” have sometimes been used in the art as synonymousterms to define an animal, the genetic contents of which has beenmodified to contain one or more exogenous nucleic acid segments.

[0491] Vector: A nucleic acid molecule, typically comprised of DNA,capable of replication in a host cell and/or to which another nucleicacid segment can be operatively linked so as to bring about replicationof the attached segment. A plasmid, cosmid, or a virus is an exemplaryvector.

[0492] The terms “substantially corresponds to”, “substantiallyhomologous”, or “substantial identity” as used herein denotes acharacteristic of a nucleic acid or an amino acid sequence, wherein aselected nucleic acid or amino acid sequence has at least about 70 orabout 75 percent sequence identity as compared to a selected referencenucleic acid or amino acid sequence. More typically, the selectedsequence and the reference sequence will have at least about 76, 77, 78,79, 80, 81, 82, 83, 84 or even 85 percent sequence identity, and morepreferably at least about 86, 87, 88, 89, 90, 91, 92, 93, 94, or 95percent sequence identity. More preferably still, highly homologoussequences often share greater than at least about 96, 97, 98, or 99percent sequence identity between the selected sequence and thereference sequence to which it was compared. The percentage of sequenceidentity may be calculated over the entire length of the sequences to becompared, or may be calculated by excluding small deletions or additionswhich total less than about 25 percent or so of the chosen referencesequence. The reference sequence may be a subset of a larger sequence,such as a portion of a gene or flanking sequence, or a repetitiveportion of a chromosome. However, in the case of sequence homology oftwo or more polynucleotide sequences, the reference sequence willtypically comprise at least about 18-25 nucleotides, more typically atleast about 26 to 35 nucleotides, and even more typically at least about40, 50, 60, 70, 80, 90, or even 100 or so nucleotides. Desirably, whichhighly homologous fragments are desired, the extent of percent identitybetween the two sequences will be at least about 80%, preferably atleast about 85%, and more preferably about 90% or 95% or higher, asreadily determined by one or more of the sequence comparison algorithmswell-known to those of skill in the art, such as e.g., the FASTA programanalysis described by Pearson and Lipman (1988).

[0493] The term “naturally occurring” as used herein as applied to anobject refers to the fact that an object can be found in nature. Forexample, a polypeptide or polynucleotide sequence that is present in anorganism (including viruses) that can be isolated from a source innature and which has not been intentionally modified by the hand of manin a laboratory is naturally-occurring. As used herein, laboratorystrains of rodents that may have been selectively bred according toclassical genetics are considered naturally occurring animals.

[0494] As used herein, a “heterologous” is defined in relation to apredetermined referenced gene sequence. For example, with respect to astructural gene sequence, a heterologous promoter is defined as apromoter which does not naturally occur adjacent to the referencedstructural gene, but which is positioned by laboratory manipulation.Likewise, a heterologous gene or nucleic acid segment is defined as agene or segment that does not naturally occur adjacent to the referencedpromoter and/or enhancer elements.

[0495] “Transcriptional regulatory element” refers to a polynucleotidesequence that activates transcription alone or in combination with oneor more other nucleic acid sequences. A transcriptional regulatoryelement can, for example, comprise one or more promoters, one or moreresponse elements, one or more negative regulatory elements, and/or oneor more enhancers.

[0496] As used herein, a “transcription factor recognition site” and a“transcription factor binding site” refer to a polynucleotidesequence(s) or sequence motif(s) which are identified as being sites forthe sequence-specific interaction of one or more transcription factors,frequently taking the form of direct protein-DNA binding. Typically,transcription factor binding sites can be identified by DNAfootprinting, gel mobility shift assays, and the like, and/or can bepredicted on the basis of known consensus sequence motifs, or by othermethods known to those of skill in the art.

[0497] As used herein, the term “operably linked” refers to a linkage oftwo or more polynucleotides or two or more nucleic acid sequences in afunctional relationship. A nucleic acid is “operably linked” when it isplaced into a functional relationship with another nucleic acidsequence. For instance, a promoter or enhancer is operably linked to acoding sequence if it affects the transcription of the coding sequence.Operably linked means that the DNA sequences being linked are typicallycontiguous and, where necessary to join two protein coding regions,contiguous and in reading frame. However, since enhancers generallyfunction when separated from the promoter by several kilobases andintronic sequences may be of variable lengths, some polynucleotideelements may be operably linked but not contiguous.

[0498] “Transcriptional unit” refers to a polynucleotide sequence thatcomprises at least a first structural gene operably linked to at least afirst cis-acting promoter sequence and optionally linked operably to oneor more other cis-acting nucleic acid sequences necessary for efficienttranscription of the structural gene sequences, and at least a firstdistal regulatory element as may be required for the appropriatetissue-specific and developmental transcription of the structural genesequence operably positioned under the control of the promoter and/orenhancer elements, as well as any additional cis sequences that arenecessary for efficient transcription and translation (e.g.,polyadenylation site(s), mRNA stability controlling sequence(s), etc.

[0499] As noted above, the present invention is generally directed tocompositions and methods for using the compositions, for example in thetherapy and diagnosis of cancer, such as hematological malignancy.Certain illustrative compositions described herein include hematologicalmalignancy-related tumor polypeptides, polynucleotides encoding suchpolypeptides, binding agents such as antibodies, antigen presentingcells (APCs) and/or immune system cells (e.g., T cells). A“hematological malignancy-related tumor protein,” as the term is usedherein, refers generally to a protein that is expressed in hematologicalmalignancy-related tumor cells at a level that is at least two fold, andpreferably at least five fold, greater than the level of expression in anormal tissue, as determined using a representative assay providedherein. Certain hematological malignancy-related tumor proteins aretumor proteins that react detectably (within an immunoassay, such as anELISA or Western blot) with antisera of a patient afflicted withhematological malignancy.

[0500] 4.28 Biological Functional Equivalents

[0501] Modification and changes may be made in the structure of thepolynucleotides and peptides of the present invention and still obtain afunctional molecule that encodes a peptide with desirablecharacteristics, or still obtain a genetic construct with the desirableexpression specificity and/or properties. As it is often desirable tointroduce one or more mutations into a specific polynucleotide sequence,various means of introducing mutations into a polynucleotide or peptidesequence known to those of skill in the art may be employed for thepreparation of heterologous sequences that may be introduced into theselected cell or animal species. In certain circumstances, the resultingencoded peptide sequence is altered by this mutation, or in other cases,the sequence of the peptide is unchanged by one or more mutations in theencoding polynucleotide. In other circumstances, one or more changes areintroduced into the promoter and/or enhancer regions of thepolynucleotide constructs to alter the activity, or specificity of theexpression elements and thus alter the expression of the heterologoustherapeutic nucleic acid segment operably positioned under the controlof the elements.

[0502] When it is desirable to alter the amino acid sequence of one ormore of the heterologous peptides encoded by the expression construct tocreate an equivalent, or even an improved, second-generation molecules,the amino acid changes may be achieved by changing one or more of thecodons of the encoding DNA sequence, according to Table 1.

[0503] For example, certain amino acids may be substituted for otheramino acids in a protein structure without appreciable loss ofinteractive binding capacity with structures such as, for example,antigen-binding regions of antibodies or binding sites on substratemolecules. Since it is the interactive capacity and nature of a proteinthat defines that protein's biological functional activity, certainamino acid sequence substitutions can be made in a protein sequence,and, of course, its underlying DNA coding sequence, and neverthelessobtain a protein with like properties. It is thus contemplated by theinventors that various changes may be made in the peptide sequences ofthe disclosed compositions, or corresponding DNA sequences which encodesaid peptides without appreciable loss of their biological utility oractivity. TABLE 1 Amino Acids Codons Alanine Ala A GCA GCC GCG GCUCysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic acid Glu EGAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA GGC GGG GGUHistidine His H CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAAAAG Leucine Leu L UUA UUG CUA CUC CUG CUU Methionine Met M AUGAsparagine Asn N AAC AAU Proline Pro P CCA CCC CCG CCU Glutamine Gln QCAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCAUCC UCG UCU Threonine Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUUTryptophan Trp W UGG Tyrosine Tyr Y UAC UAU

[0504] In making such changes, the hydropathic index of amino acids maybe considered. The importance of the hydropathic amino acid index inconferring interactive biologic function on a protein is generallyunderstood in the art (Kyte and Doolittle, 1982, incorporate herein byreference). It is accepted that the relative hydropathic character ofthe amino acid contributes to the secondary structure of the resultantprotein, which in turn defines the interaction of the protein with othermolecules, for example, enzymes, substrates, receptors, DNA, antibodies,antigens, and the like. Each amino acid has been assigned a hydropathicindex on the basis of their hydrophobicity and charge characteristics(Kyte and Doolittle, 1982), these are: isoleucine (+4.5); valine (+4.2);leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5);methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7);serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6);histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5);asparagine (−3.5); lysine (−3.9); and arginine (−4.5).

[0505] It is known in the art that certain amino acids may besubstituted by other amino acids having a similar hydropathic index orscore and still result in a protein with similar biological activity,i.e. still obtain a biological functionally equivalent protein. Inmaking such changes, the substitution of amino acids whose hydropathicindices are within ±2 is preferred, those that are within ±1 areparticularly preferred, and those within ±0.5 are even more particularlypreferred. It is also understood in the art that the substitution oflike amino acids can be made effectively on the basis of hydrophilicity.U.S. Pat. No. 4,554,101, incorporated herein by reference, states thatthe greatest local average hydrophilicity of a protein, as governed bythe hydrophilicity of its adjacent amino acids, correlates with abiological property of the protein.

[0506] As detailed in U.S. Pat. No. 4,554,101, the followinghydrophilicity values have been assigned to amino acid residues:arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1);serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0);threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5);cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8);isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan(−3.4). It is understood that an amino acid can be substituted foranother having a similar hydrophilicity value and still obtain abiologically equivalent, and in particular, an immunologicallyequivalent protein. In such changes, the substitution of amino acidswhose hydrophilicity values are within ±2 is preferred, those that arewithin ±1 are particularly preferred, and those within ±0.5 are evenmore particularly preferred.

[0507] As outlined above, amino acid substitutions are generallytherefore based on the relative similarity of the amino acid side-chainsubstituents, for example, their hydrophobicity, hydrophilicity, charge,size, and the like. Exemplary substitutions which take several of theforegoing characteristics into consideration are well known to those ofskill in the art and include: arginine and lysine; glutamate andaspartate; serine and threonine; glutamine and asparagine; and valine,leucine and isoleucine.

5. EXAMPLES

[0508] The following examples are included to demonstrate preferredembodiments of the invention. However, those of skill in the art should,in light of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention described in the appended claims.

5.1 Example 1 Identification of Hematological Malignancy-Related AntigenPolynucleotides

[0509] This Example illustrates the identification of hematologicalmalignancy-related antigen polynucleotides from non-Hodgkin's lymphomas.

[0510] Hematological malignancy-related antigen polynucleotides wereisolated by PCR-based subtraction. PolyA mRNA was prepared from T cellnon-Hodgkin's lymphomas, B cell non-Hodgkin's lymphomas and normaltissues. Six cDNA libraries were constructed, PCR-subtracted andanalyzed. Two libraries were constructed using pools of three T cellnon-Hodgkin's lymphoma mRNAs (referred to herein as TCS libraries). Twoothers were constructed using pools of three B cell non-Hodgkin'slymphoma mRNAs (referred to herein as BCNHL libraries). Two otherlibraries were constructed using a pool of 2 Hodgkin's lymphoma mRNAs(referred to herein as HLS libraries. cDNA synthesis, hybridization andPCR amplification were performed according to Clontech's user manual(PCR-Select cDNA Subtraction), with the following changes: 1) cDNA wasrestricted with a mixture of enzymes, including MscI, PvuII, StuI andDraI, instead of the single enzyme RsaI; and 2) the ratio of driver totester cDNA was increased in the hybridization steps (to 76:1) to give amore stringent subtraction.

[0511] The two TCS libraries were independently subtracted withdifferent pools of driver cDNAs. Driver #1 contained cDNA prepared fromspecific normal tissues (lymph node, bone marrow, T cells, heart andbrain), and this subtraction generated the library TCS-D1 (T cellnon-Hodgkin's lymphoma subtracted library with driver #1). Driver #2contained non-specific normal tissues (colon, large intestine, lung,pancreas, spinal cord, skeletal muscle, liver, kidney, skin and brain),and this subtraction generated the library TCS-D2 (T cell non-Hodgkin'slymphoma subtraction library with driver #2).

[0512] Similarly, the two BCNHL libraries were independently subtractedwith different pools of driver cDNAs. Driver #1 contained cDNA preparedfrom specific normal tissues (lymph node, bone marrow, B cells, heartand brain), and this subtraction generated the library BCNHL/D1 (B cellnon-Hodgkin's lymphoma subtracted library with driver #1). Driver #2contained non-specific normal tissues (brain, lung, pancreas, spinalcord, skeletal muscle, colon, spleen, large intestine and PBMC), andthis subtraction generated the library BCNHL/D2 (B cell non-Hodgkin'slymphoma subtraction library with driver #2).

[0513] The two HLS libraries were independently subtracted withdifferent pools of driver cDNAs. Driver #1 contained cDNA prepared fromspecific normal tissues (lymph node, bone marrow, B cells and lung) andthis subtraction generated HLS-D1 (Hodgkin's lymphoma subtractionlibrary with driver #1). Driver #2 contained non-specific normal tissues(colon, large intestine, lung, pancreas, spinal cord, skeletal muscle,liver, kidney, skin and brain) and this generated the library HLS-D2(Hodgkin's lymphoma subtraction library with driver #2).

[0514] To analyze the efficiency of the subtraction, actin (ahousekeeping gene) was PCR amplified from dilutions of subtracted aswell as unsubtracted PCR samples. Furthermore, the complexity andredundancy of each library was characterized by sequencing 96 clonesfrom each of the PCR subtraction libraries (TCS-D1, TCS-D2, BCNHL/D1,BCNHL/D2, HLS-D1 and HLS-D2). These analyses indicated that thelibraries are enriched for genes overexpressed in leukemia tissues andspecifically T cell and B cell non-Hodgkin's lymphoma and M. Hodgkin'slymphoma samples.

[0515] Following PCR amplification, the cDNAs were cloned into thepCR2.1-TOPO plasmid vector (Invitrogen).

[0516] Sequences obtained from these analyses were searched againstknown sequences in the publicly available databases using the BLAST 2.0release. The default BLAST parameters used were as follows: GAPPARAMETERS: Open Gap=0, Extended Gap=0; OUTPUT PARAMETERS: Expect=10.0,Threshold=0, Number of Alignments=250; For BLASTN, the search parameterswere as follows: Mismatch=−3, Reward=1, Word size=0. The alignments werepresented pair-wise, with a window percent identity=22. All availableprotein and nucleotide databases were searched, including, PIR,SwissPROT, GenBank, Mouse EST, Human EST, Other EST, Human repeat andhigh throughput sequences, and published patents and patent applicationdatabase.

[0517] From these, a number of unique sequences were identified thatrepresented novel polynucleotide sequences that had not previously beendescribed in the GenBank and other sequence databases. A number of othersequences were identified that appeared to contain significant homologywith one or more sequences previously identified in the databases,although they were described only as genomic or cDNA clones, and had noknown function. The remaining sequences corresponded to known genes. Theclones obtained from this analysis are summarized in Tables 2-6 inco-pending application U.S. Ser. No. 09/796,692.

5.2 Example 2 Analysis of Subtracted cDNA Sequences by MicroarrayAnalysis

[0518] Subtracted cDNA sequences were analyzed by microarray analysis toevaluate their expression in hematological malignancies and normaltissues. Using this approach, cDNA sequences were PCR amplified andtheir mRNA expression profiles in hematological malignancies and normaltissues are examined using cDNA microarray technology essentially asdescribed (Shena et al., 1995).

[0519] In brief, the clones identified from the subtracted cDNAlibraries analyses were immobilized and arrayed onto glass slides asmultiple replicas on microarray slides and the slides were hybridizedwith two different sets of probes, with each location on the microarrayslide corresponding to a unique cDNA clone (as many as 5500 clones canbe arrayed on a single slide, or chip). Each chip is hybridized with apair of cDNA probes that are fluorescence-labeled with Cy3 and Cy5,respectively. The set of probes derived from the hematologicalmalignancies was labeled with cy3 while the other set of probes derivedfrom a pool of normal tissues was labeled with cy5. Typically, 1 μg ofpolyA⁺ RNA was used to generate each cDNA probe. After hybridization,the chips were scanned and the fluorescence intensity recorded for bothCy3 and Cy5 channels. The difference in intensities (i.e., cy3/cy5ratios) following hybridization with both probe sets provided theinformation on the relative expression level of each cDNA sequencesimmobilized on the slide in tumor versus normal tissues. There aremultiple built-in quality control steps. First, the probe quality ismonitored using a panel of ubiquitously expressed genes. Secondly, thecontrol plate also can include yeast DNA fragments of whichcomplementary RNA may be spiked into the probe synthesis for measuringthe quality of the probe and the sensitivity of the analysis. Thismethodology provides a sensitivity of 1 in 100,000 copies of mRNA, andthe reproducibility of the technology may be ensured by includingduplicated control cDNA elements at different locations.

[0520] Analysis of hematological malignancy subtracted clones bymicroarray analyses on a variety of microarray chips identified thesequences set forth in SEQ ID NO:1 through SEQ ID NO:664 of the instantapplication and co-pending application U.S. Ser. No. 09/796,692 as beingat least two-fold overexpressed in hematological malignancies versusnormal tissues.

5.3 Example 3 Polynucleotide and Polypeptide Compositions: BriefDescription of the cDNA Clones and Open Reading Frames Identified bySubtractive Hybridization and Microarray Analysis

[0521] Table 7 in co-pending application U.S. Ser. No. 09/796,692 liststhe sequences of the polynucleotides obtained during the analyses of thepresent invention. Shown are the 664 polynucleotide sequences, alongwith their clone name identifiers, as well as the serial number andfiling date of the priority provisional patent application in which theclone was first identified. Also listed in Table 7 are the TCL1 DNA andprotein (SEQ ID NOs:665 and 666) and Coronin 1A DNA and protein (SEQ IDNOs:667 and 668).

[0522] Table 8 in co-pending application U.S. Ser. No. 09/796,692identifies the putative open reading frames obtained from analyses ofthe cDNA sequences obtained in SEQ ID NO:1-SEQ ID NO:664 as describedabove. Shown are the sequence identifiers, the clone name andtranslation frame, and the start and stop nucleotides in thecorresponding DNA sequence used to generate the polypeptide sequence ofthe open reading frame (SEQ ID NOs:669-2532).

[0523] Table 9 in co-pending application U.S. Ser. No. 09/796,692identifies an additional set of particular hematologicalmalignancy-related cDNA sequences that were obtained using thesubtractive library and microarray methods as described above. Thesesequences, designated SEQ ID NO:2533-SEQ ID NO:9597 in the instantapplication and co-pending application U.S. Ser. No. 09/796,692 areshown in the Table along with the original clone name, and the serialnumber and filing date of the priority provisional application in whichthe clone was first described.

5.4 Example 4 Identification of a Specific Gene, LY1448, Associated withB Cell Leukemias, Lymphomas and Multiple Myelomas

[0524] This example illustrates the identification of a specific gene,and its encoded protein that is associated with B cell leukemias,lymphomas and multiple myelomas.

[0525] SEQ ID NO:9599, also termed “Ly1448,” a portion of which wasdisclosed earlier in co-pending application U.S. Ser. No. 09/796,692 asSEQ ID NO:636 was used to screen a series of MicroArray and RealTimechips and panels containing cDNAs made from RNAs isolated from normalcells and hematologically malignant cells. SEQ ID NO:9599 appeared to beexpressed in normal B cell lines, CD 19⁺ cell lines, and highlyexpressed in a subset of Non-Hodgkins B-cell lymphoma cell lines,Hodgkins lymphoma cell lines, follicular lymphoma cell lines, andChronic Lymphocytic Leukemia cell lines.

[0526] SEQ ID NO:9599, which is a 523 base pair cDNA fragment, was usedto screen the LIFESEQ® Gold database and two additional clones wereidentified, SEQ ID NO:9598, also termed “LS 1384258.1”, which is a 622base pair cDNA fragment, and SEQ ID NO:9600, also termed “LS 368109.1”,which is a 1,908 base pair cDNA.

[0527] Both SEQ ID NOs:9598 and 9600 were used to screen the publiclyavailable human genome database and homologous sequences were identifiedon human chromosome 1. Exons and introns were identified by comparingthe publicly available genomic sequence data to SEQ ID NOs:9598-9600 andare shown diagrammatically in FIG. 6. This comparison determined thatSEQ ID NO:9600 contained 16 exons. Open reading frames were identifiedby a LIFESEQ® Gold BLAST analysis. These results are also showndiagrammatically in FIG. 6. SEQ ID NO:9600 is a full length clonecomprising 8 untranslated exons (exons 1-8) and 8 exons containing openreading frames (exons 9-16). SEQ ID NOs:9598 and 9599 are fragments ofalternatively spliced variants of SEQ ID NO:9600.

[0528] The BLAST analysis determined that the open reading frame (ORF)of SEQ ID NO:9600 begins at nucleotide 777, ends at nucleotide 1562 andencodes a 261 amino acid protein as identified in SEQ ID NO:9611, termedLY1448 protein. Further analysis of SEQ ID NO:9600 using both TMpred andPSORTII indicated that SEQ ID NO:9611 is a type-1b membrane protein,containing a predicted transmembrane domain beginning at amino acid 156and ending at amino acid 177. The extracellular portion of SEQ IDNO:9611 has homology with immunoglobulins and contains a predictedIg-like domain. The intracellular portion of SEQ ID NO:9611 contains SrcHomology-2 (SH2) binding domains and an Immune Receptor Tyrosine-BasedInhibition Motif (ITIM). As such, LY1448 protein may play a specificrole in hematopoetic cell signaling.

[0529] A BLAST search of GenBank determined that LY1448 protein sharedhomology with a recently identified protein, SH2 domain-containingphosphatase anchor protein 1 a (SPAPla), Xu et al., Biochem. Biophys.Res. Commun. 280: 768-775 (2001). The nucleic acid sequence encodingSPAP1a is 1329 nucleotides long (SEQ ID NO:9601) and encodes a protein255 amino acids long (SEQ ID NO:9612). TMpred and PSORTII analysis ofthe nucleotide sequence encoding SPAP1a indicates that SPAP1a containstwo predicted transmembrane domains. The first predicted transmembranedomain begins at amino acid 32 and extends to amino acid 53. The secondpredicted transmembrane domain begins at amino acid 150 and extends toamino acid 171.

[0530] A comparison of the nucleotide sequence, SEQ ID NO:9600, encodingLY1448 protein and the nucleotide sequence, SEQ ID NO:9601, encodingSPAPla shows that the first 919 nucleotides and the first 447nucleotides respectively are unique to each sequence. The remainingnucleotides of each sequence are highly homologous. Similarly, acomparison of the amino acid sequence of LY1448 protein (SEQ ID NO:9611)and the amino acid sequence of SPAP1 (SEQ ID NO:9612) shows that thefirst 48 amino acids of LY1448 and the first 42 amino acids of SPAP1aare unique to each protein. The remaining 213 amino acids of eachprotein, comprising a portion of the extracellular domain, thetransmembrane domain, and the intracellular domain are identical. Thesedata suggest that LY1448 and SPAP1a may be novel splice variants of eachother. Due to the differences in amino acid sequence between the twoproteins, SPAP1a does not contain the unique Ig-like domain observed inLY1448.

[0531] A BLASTX search of both the GenBank and GenSeq databasesindicated that LY1448 and SPAPla also share homology with theImmunoglobulin Receptor Translocation Associated Protein 4 (“IRTA4”)whose nucleotide sequence is represented in SEQ ID NO:9609, and whoseamino acid sequence is represented in SEQ ID NO:10464. Nucleotides 1-630of SEQ ID NO:9600 encoding a portion of the 5′ untranslated region ofthe LY1448 cDNA are unique to LY1448. The remaining nucleotides arehighly homologous to the IRTA4 nucleotide sequence. Nucleotides 1-642 ofSEQ ID NO:9609 are unique to the IRTA4 nucleotide sequence. The aminoterminal 247 amino acids of the IRTA4 protein represented in SEQ IDNO:10464 are unique to IRTA4. The remaining amino acids of the IRTA4protein are highly homologous to the LY1448 protein. These data suggestthat LY1448 and IRTA4 may be novel splice variants of each other.

[0532] LY1448 protein immunogenic peptides comprising 5 non-overlapping31mer or 32mer amino acid fragments (SEQ ID NOs:9613-9617) of theextracellular domain LY1448 protein (amino acids 1-156 of SEQ IDNO:9611) were generated and are being used to generate antibodiesspecific for the LY1448 protein. These antibodies will be useful inrecognizing LY1448 protein for diagnostic and therapeutic use in bothnormal and diseased cells. Each peptide fragment used to generateantibodies also contains a GCG peptide linker sequence at thecarboxy-terminus of the fragment. These antibodies may also recognizethe IRTA4 protein. Antibodies immunoreactive to epitopes present onpeptides defined by SEQ ID NOs:9614-9617 may also recognize epitopespresent in SPAPla.

[0533] Seventeen overlapping immunogenic peptides derived from LY1448protein sequence were also generated. 16-30mer amino acid peptides weregenerated, each peptide contains sequential amino acid sequences andoverlaps peptides containing adjacent sequences by 15 amino acids (SEQID NOs:10438-10453). One peptide encoding the carboxy-terminus of LY1448protein is 21 amino acids long and also overlaps the adjacent peptide by15 amino acids (SEQ ID NO:10454). These seventeen peptides will also beused to generate antibodies immunoreactive to epitopes present on thepeptides. Antibodies which recognize epitopes present on peptidesidentified by SEQ ID NOs:10438 and 10439 will recognize LY1448 proteinwhereas antibodies which recognize epitopes present on peptidesidentified by SEQ ID NOs:10440-10454 may recognize both LY1448 andSPAP1a proteins. Antibodies generated against all of these peptides mayalso recognize IRTA4. Antibodies generated against these 17 overlappingpeptides will be useful for both diagnostic and therapeutic purposes.

5.5 Example 5 Identification of LY1448 Immungenic Peptides

[0534] This example illustrates the identification of peptides usefulfor generating cytotoxic T cell or helper T cell responses.

[0535] LY1448 protein peptides useful for generating a cellular immuneresponse were identified. Preferred epitope binding motifs for many ofthe HLA class I and class II molecules are known. The LY1448 amino acidsequence was searched for peptides that would bind to the specific HLAmolecules identified in Table 10. 9mer peptides predicted to bind toeach of the specific HLA molecules were identified and SEQ ID NOscorresponding to the peptides which bind to each HLA molecule areindicated. TABLE 10 LY1448 CTL Peptides Identified HLA molecule selectedLY1448 peptides identified HLA A_0201 SEQ ID NOs: 9618-9637 HLA A_0205SEQ ID NOs: 9638-9657 HLA A24 SEQ ID NOs: 9658-9677 HLA A3 SEQ ID NOs:9678-9697 HLA A68.1 SEQ ID NOs: 9698-9717 HLA A_1101 SEQ ID NOs:9718-9737 HLA A_3101 SEQ ID NOs: 9738-9757 HLA A_3302 SEQ ID NOs:9758-9777 HLA B14 SEQ ID NOs: 9778-9797 HLA B40 SEQ ID NOs: 9798-9817HLA B60 SEQ ID NOs: 9818-9837 HLA B61 SEQ ID NOs: 9838-9857 HLA B62 SEQID NOs: 9858-9877 HLA B7 SEQ ID NOs: 9878-9897 HLA B8 SEQ ID NOs:9898-9917 HLA B_2702 SEQ ID NOs: 9918-9937 HLA B_2705 SEQ ID NOs:9938-9957 HLA B_3501 SEQ ID NOs: 9958-9977 HLA B_3701 SEQ ID NOs:9978-9997 HLA B_3801 SEQ ID NOs: 9998-10017 HLA B_3901 SEQ ID NOs:10018-10037 HLA B_3902 SEQ ID NOs: 10038-10057 HLA B_4403 SEQ ID NOs:10058-10077 HLA B_5101 SEQ ID NOs: 10078-10097 HLA B_5102 SEQ ID NOs:10098-10117 HLA B_5103 SEQ ID NOs: 10118-10137 HLA B_5201 SEQ ID NOs:10138-10157 HLA B_5801 SEQ ID NOs: 10158-10177 HLA Cw_0301 SEQ ID NOs:10178-10197 HLA Cw_0401 SEQ ID NOs: 10198-10217 HLA Cw_0602 SEQ ID NOs:10218-10237 HLA Cw_0702 SEQ ID NOs: 10238-10257 HLA Db SEQ ID NOs:10258-10277 HLA Db_revised SEQ ID NOs: 10278-10297 HLA Dd SEQ ID NOs:10298-10317 HLA Kb SEQ ID NOs: 10318-10337 HLA Kd SEQ ID NOs:10338-10357 HLA Kk SEQ ID NOs: 10358-10377 HLA Kk SEQ ID NOs:10378-10397 HLA Ld SEQ ID NOs: 10398-10417 HLA Cattle_A20 SEQ ID NOs:10418-10437

[0536] The location of additional immunogenic peptides was determined byanalyzing the complete LY1448 protein amino acid sequence of SEQ IDNO:9611 using the program TSITES. The results are shown in FIG. 7.TSITES identified the location of predicted amphipathic helices (A), thelocation of amino acid residues matching the Rothbard/Taylor motif (R),the location of residues matching the IAd motif (D) and the location ofresidues matching the IEd motif (d). Based on this analysis, fouradditional peptides were identified that are predicted to containepitopes that will bind to CD4⁺ T cells. Peptide 1 spans amino acids40-78 of the LY1448 protein and is represented by SEQ ID NO:10455.Peptide 2 spans amino acids 127-150 of the LY 1448 protein and isrepresented by SEQ ID NO:10456. Peptide 3 spans amino acids 210-233 ofthe LY 1448 protein and is represented by SEQ ID NO:10457. Peptide 4spans amino acids 141-178 of the LY 1448 protein and is represented bySEQ ID NO:10458.

5.6 EXAMPLE 6 LY1448 Protein is a Cell Surface Protein

[0537] This example illustrates that the LY1448 protein encoded by SEQID NO:9600 is a cell surface protein.

[0538] The nucleotide sequence encoding LY1448 was sub-cloned in to themammalian expression vector pCEP4 (Invitrogen) as follows. The portionof SEQ ID NO:9600 encoding the LY1448 protein was PCR amplified using asense amplimer comprising nucleotides 777-800 of SEQ ID NO:9600 andadditional nucleotides on the 5′ end which contained a HindIIIrestriction enzyme site and an anti-sense primer comprising nucleotides1544-1570 of SEQ ID NO:9600 and additional nucleotides on the 3′endwhich contained a NotI restriction enzyme site. The PCR product wascloned into the pCR-Blunt vector (Invitrogen), and sequenced. DNA from apCR-Blunt clone with the correct sequence was digested with HindIII andNotI to release the LY1448 cDNA insert and subcloned into the mammalianexpression vector pCEP4 (Invitrogen) which had been previously modifiedto contain a c-terminal FLAG epitope tag (Sigma; amino acid sequenceDYKDDDDK; SEQ ID NO:10467). The resulting recombinant vectorLY1448-FLAG/pCEP encoded a LY1448-FLAG fusion protein.

[0539] To determine if the recombinant expression vectorLY1448-FLAG/pCEP would express protein, the recombinant vector wastransiently transfected into HEK293 cells using Lipofectamine 2000according to manufacturers instructions (GibcoBRL). Separately, HEK293cells were also transfected with a control vector containing arecombinant FLAG construct and non-recombinant pCEP4 vector. Transfectedcells were cultured for 48 hours and then whole cell lysates wereprepared. Lysates were run on a polyacrylamide gel, and the gel waselectroblotted onto nitrocellulose membrane using standard techniques(Ausubel et al.,). The electroblot was probed with a mouse anti-FLAGmonoclonal antibody and binding of the mouse mAb was detected with abiotinylated rabbit anti-mouse IgG and developed with avidin-HRP and ECLreagent and the results are shown in FIG. 8. Lanes 2 and 3 are controllanes and lane 4 contains the whole cell extract of cells transfectedwith LY1448-FLAG/pCEP4. Anti-FLAG antibodies recognized a LY1448-FLAGfusion protein of the expected molecular weight.

[0540] To determine if recombinant LY1448 protein was present on thecell surface, whole cells transiently transfected with LY1448-FLAG/pCEP4were biotinylated with Biotin-7-NHS, cells were washed and whole celllysates were generated in TRITON X-100 lysis buffer. Lysates wereimmunoprecipitated with anti-FLAG Sepharose and the resultingimmunoprecipitated material was run on a polyacrylamide gel. The gel waselectroblotted onto nitrocellulose membrane and the blot was developedwith avidin-HRP and ECL reagent. The results are shown in FIG. 9. Lane 1contains lysate derived from cells transfected with non-recombinantvector and lane 2 contains lysate from cells transfected with vectorexpressing LY1448-FLAG fusion protein. The data show that a proteinprecipitable with anti-FLAG sepharose of the expected molecular weightfor a LY1448-FLAG fusion protein was biotinylated in a whole cell assayindicating that LY1448 is found on the cell surface.

5.7 Example 7 Identification of Two Specific Genes, LY1447 and LY1481are Associated with B Cell Leukemias, Lymphomas and Multiple Myelomas

[0541] This example illustrates the identification of two specific genesthat are associated with B cell leukemias, lymphomas and multiplemyelomas.

[0542] LY1447 and LY1481, portions of which were disclosed earlier inco-pending application U.S. Ser. No. 09/796,692, are cDNAs alsoassociated with B cell leukemias, lymphomas and multiple myelomas. Thenucleotide sequence of LY1447 is disclosed herein as SEQ ID NO:9602. Thenucleotide sequence of LY1481 is disclosed herein as SEQ ID NO:9603. Theamino acid sequence encoded by SEQ ID NO:9603 is disclosed herein as SEQID NO:10466.

[0543] SEQ ID NOs:9602 and 9603 were used in BLASTX searches of bothGenBank and GeneSEQ databases. Homologous sequences were only found inthe GeneSEQ database. This analysis showed that SEQ ID NO:9602 washomologous to the 3′ untranslated region of the IRTA2c gene onchromosome 1. SEQ ID NO:9603 was homologous to a portion of the codingregion of IRTA3 also on chromosome 1.

[0544] The IRTA superfamily of genes comprises IRTA 1, 2a, 2b, 2c, 3, 4,and 5, whose nucleic acid sequences are disclosed herein as SEQ IDNOs:9604-9610 respectively and whose corresponding amino acid sequencesare disclosed herein as SEQ ID NOs:10459-10465 respectively. These IRTAgenes are located on chromosome 1 (q21) and are associated withchromosomal translocations. These translocations combine a portion ofchromosome 1 with a portion of chromosome 14 (q32). This portion ofchromosome 14 is the location of the genes encoding the immunoglobulinproteins. These chromosomal translocations are associated with various Bcell leukemias, lymphomas and multiple myelomas.

5.8 Example 8 Generation of Polyclonal Antisera which Recognizes LY1448Recombinant Protein and Two Peptides

[0545] This example illustrates the production of recombinant LY1448protein in E. coli. This example further illustrates the production ofanti-sera against that recombinant protein and two synthetic peptideswhich comprise portions of the LY1448 extracellular domain.

[0546] The nucleotide sequence encoding LY1448 (nucleotides 780-1573 ofSEQ ID NO:9600) were cloned into the E. coli expression vector pET 28which had been modified to include nucleotides encoding an initiationmethionine residue, a glutamine residue and a six amino acid histidinetag adjacent to transcription initiation sequences of the vector. PCRprimers comprising nucleotide sequences 780-801 (sense) and 1559-1573(antisense) of SEQ ID NO:9600 were used to amplify a nucleotide sequenceencoding amino acids 2-261 of SEQ ID NO:9611 using standard techniques(Sambrook et al., supra and Ausubel et al., supra). The antisense primeralso contained a XhoI restriction enzyme site to facilitate cloning. Theresulting PCR product was digested with XhoI and ligated into themodified pET 28 which had been digested with Eco 721 and XhoI. Therecombinant clone was used to transform BLR (DE3) pLys S and HMS 174pLys S bacteria. LY1448 protein was purified from recombinant bacterialcultures. LY1448 protein was purified from cell lysates by Ni columnchromatography (Qiagen), followed by anion exchange chromatography andanti-his affinity chromatography steps.

[0547] The resulting purified recombinant LY1448 protein and KLH(keyhole limpet hemocyanin) conjugated, 31-mer peptides corresponding tothe LY1448 amino acids 1 to 31 (SEQ ID NO:9613)(MGKKTQRSLSAELEIPAVKESDAGKYYCRADGCG-KLH) (peptide 1) and 63 to 93 (SEQID NO:9615) (QAAVGDLLELHCEALRGSPPILYQFYHEDVTGCG-KLH) (peptide 3) wereinjected into rabbits using the following scheme: day 0: 0.15 mg/rabbit,in CFA, (complete Freund's adjuvant) s.c., day 21:0.15 mg/rabbit, inIFA, (incomplete Freund's adjuvant) s.c., day 35:0.15 mg/rabbit, in IFA,s.c., day 42:production bleed (˜20 mL). Rabbits 1448-1a and 1b receivedrecombinant LY1448, rabbits 1448-2a and 2b received peptide 1, andrabbits 1448-3a and 3b received peptide 3.

[0548] For ELISA analysis of antigen specificity, rabbit sera weretitered against antigen-coated (0.1 mg/well) 96-well microtiter plates.Samples were diluted initially at 1:100, and then serially diluted 3fold and added to the plates in duplicate. Antigen specific binding ofrabbit IgG to the plate was revealed by goat anti-rabbit IgG (H+L)-HRPconjugate, and the plates were developed with TMB substrate and read atOD450 nm on a microplate reader. For FACS analysis, HEK293 andLyl448/HEK293 cells (supra) were collected and washed with ice coldstaining buffer (PBS+1% BSA+Sodium Azide). Next, the cells wereresuspended in 50 ul staining buffer and incubated for 30 minutes on icewith 75 ul of rabbit anti-Lyl448P recombinant or peptide sera diluted1:500. Pre-bleed sera was used at the same concentration as a negativecontrol. The cells were washed 3 times with staining buffer and thenincubated with a 1:100 dilution of a goat anti-rabbit Ig(H+L)-FITCreagent (Southern Biotechnology) for 30 minutes on ice. Following 3washes, the cells were resuspended in staining buffer containingPropidium Iodide (PI), a vital stain that allows for identification ofpermeable cells, and analyzed by FACS.

[0549] The results of the FACS analysis show that the polyclonalantisera raised against the full length recombinant protein (anti-LY1448antisera) and both synthetic peptides (anti-peptide anti-sera) were ableto recognize and bind to full length, native LY1448 expressed in HEK293transfectants. Pre-immunization (pre-bleed) antisera obtained from theeach rabbit did not bind to the LY1448/HEK293 expressing cells.Similarly, anti-LY1448 and anti-peptide antisera did not bind to controlHEK293 cells.

[0550] The results of the ELISA assys show that anti-LY1448 antiseraraised were able to bind strongly to immobilized recombinant LY1448 andpeptide 1 (SEQ ID NO:9613) and bind weakly to the peptide 3 (SEQ IDNO:9615). Polyclonal antisera (anti-peptide 1) raised against thesynthetic peptide 1 (SEQ ID NO:9613) bound strongly to peptide 1 (SEQ IDNO:9613) and recombinant LY1448 protein, and did not bind at all topeptide 3 (SEQ ID NO:9615). Polyclonal antisera (anti-peptide 3) raisedagainst the synthetic peptide 3 (SEQ ID NO:9615) bound strongly topeptide 3 (SEQ ID NO:9615) and the recombinant LY1448 protein.Anti-peptide 3 bound weakly to peptide 1. These results indicate thatthe anti-LY1448 antisera and the anti-peptide antisera recognizeepitopes present on LY1448 and would be useful for both therapeutic anddiagnostic purposes.

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[0905] All of the compositions and methods disclosed and claimed hereincan be made and executed without undue experimentation in light of thepresent disclosure. While the compositions and methods of this inventionhave been described in terms of preferred embodiments, it will beapparent to those of skill in the art that variations may be applied tothe composition, methods and in the steps or in the sequence of steps ofthe method described herein without departing from the concept, spiritand scope of the invention. More specifically, it will be apparent thatcertain agents which are both chemically and physiologically related maybe substituted for the agents described herein while the same or similarresults would be achieved. All such similar substitutes andmodifications apparent to those skilled in the art are deemed to bewithin the spirit, scope and concept of the invention as defined by theappended claims. All publications, patents, and patent applicationscited herein are hereby incorporated by reference in their entirety forall purposes. Accordingly, the exclusive rights sought to be patentedare as described in the claims below:

0 SEQUENCE LISTING The patent application contains a lengthy “SequenceListing” section. A copy of the “Sequence Listing” is available inelectronic form from the USPTO web site(http://seqdata.uspto.gov/sequence.html?DocID=20040175739). Anelectronic copy of the “Sequence Listing” will also be available fromthe USPTO upon request and payment of the fee set forth in 37 CFR1.19(b)(3).

What is claimed is:
 1. An isolated polynucleotide encoding a proteinless than about 300 amino acids comprising a sequence selected from thegroup consisting of: (a) sequence provided in SEQ ID NO:9600; (b)complements of the sequence provided in SEQ ID NO:9600; (c) sequenceshaving at least 90% identity to a sequence of SEQ ID NO:9600; and (d)degenerate variants of a sequence provided in SEQ ID NO:9600.
 2. Anisolated polypeptide comprising an amino acid sequence selected from thegroup consisting of: (a) sequences encoded by a polynucleotide of claim1; and (b) sequences having at least 90% identity to a sequence encodedby a polynucleotide of claim 1; and (c) sequences provided in SEQ IDNO:9613-9617; and (d) sequences provided in SEQ ID NO:9618-10437; and(e) sequences provided in SEQ ID NO:10438-10458.
 3. An expression vectorcomprising a polynucleotide of claim 1 operably linked to an expressioncontrol sequence.
 4. A host cell transformed or transfected with anexpression vector according to claim
 3. 5. An isolated antibody, orantigen-binding fragment thereof, that specifically binds to apolypeptide of claim
 2. 6. A method for detecting the presence of acancer in a patient, comprising the steps of: (a) obtaining a biologicalsample from the patient; (b) contacting the biological sample with abinding agent that binds to a polypeptide of claim 2; (c) detecting inthe sample an amount of polypeptide that binds to the binding agent; and(d) comparing the amount of polypeptide to a predetermined cut-off valueand therefrom determining the presence of a cancer in the patient.
 7. Afusion protein comprising at least one polypeptide according to claim 2.8. An oligonucleotide that hybridizes to nucleotides 1-630 of thesequence recited in SEQ ID NO:9600 under moderately stringentconditions.
 9. A method for stimulating and/or expanding T cellsspecific for a tumor protein, comprising contacting T cells with atleast one component selected from the group consisting of: (a)polypeptides according to claim 2; (b) polynucleotides according toclaim 1; and (c) antigen-presenting cells that express a polypeptideaccording to claim 1, under conditions and for a time sufficient topermit the stimulation and/or expansion of T cells.
 10. An isolated Tcell population, comprising T cells prepared according to the method ofclaim
 9. 11. A composition comprising a first component selected fromthe group consisting of physiologically acceptable carriers andimmunostimulants, and a second component selected from the groupconsisting of: (a) polypeptides according to claim 2; (b)polynucleotides according to claim 1; (c) antibodies according to claim5; (d) fusion proteins according to claim 7; (e) T cell populationsaccording to claim 10; and antigen presenting cells that express apolypeptide according to claim
 2. 12. A method for stimulating an immuneresponse in a patient, comprising administering to the patient acomposition of claim
 11. 13. A method for the treatment of a cancer in apatient, comprising administering to the patient a composition of claim11.
 14. A method for determining the presence of a cancer in a patient,comprising the steps of: (a) obtaining a biological sample from thepatient; (b) contacting the biological sample with an oligonucleotideaccording to claim 8; (c) detecting in the sample an amount of apolynucleotide that hybridizes to the oligonucleotide; and (d) comparingthe amount of polynucleotide that hybridizes to the oligonucleotide to apredetermined cut-off value, and therefrom determining the presence ofthe cancer in the patient.
 15. A diagnostic kit comprising at least oneoligonucleotide according to claim
 8. 16. A diagnostic kit comprising atleast one antibody according to claim 5 and a detection reagent, whereinthe detection reagent comprises a reporter group.
 17. A method forinhibiting the development of a cancer in a patient, comprising thesteps of: (a) incubating CD4+ and/or CD8+T cells isolated from a patientwith at least one component selected from the group consisting of: (i)polypeptides according to claim 2; (ii) polynucleotides according toclaim 1; and (iii) antigen presenting cells that express a polypeptideof claim 2, such that T cell proliferate; (b) administering to thepatient an effective amount of the proliferated T cells, and therebyinhibiting the development of a cancer in the patient.
 18. An isolatedpolynucleotide encoding a protein of less than 300 amino acidscomprising a sequence selected from the group consisting of: (a)sequence provided in SEQ ID NO:9603; (b) complements of the sequencesprovided in SEQ ID NO:9603; (c) sequences having at least 90% identityto a sequence of SEQ ID NO:9603; and (d) degenerate variants of asequence provided in SEQ ID NO:9603.
 19. An isolated polypeptidecomprising an amino acid sequence selected from the group consisting of:(a) sequences encoded by a polynucleotide of claim 18; and (b) sequenceshaving at least 90% identity to a sequence encoded by a polynucleotideof claim 18; and (c) the sequence provided in SEQ ID NO:10466.
 20. Anexpression vector comprising a polynucleotide of claim 18 operablylinked to an expression control sequence.
 21. A host cell transformed ortransfected with an expression vector according to claim
 20. 22. Anisolated antibody, or antigen-binding fragment thereof, thatspecifically binds to a polypeptide of claim
 19. 23. A method fordetecting the presence of a cancer in a patient, comprising the stepsof: (a) obtaining a biological sample from the patient; (b) contactingthe biological sample with a binding agent that binds to a polypeptideof claim 19; (c) detecting in the sample an amount of polypeptide thatbinds to the binding agent; and (d) comparing the amount of polypeptideto a predetermined cut-off value and therefrom determining the presenceof a cancer in the patient.
 24. A fusion protein comprising at least onepolypeptide according to claim
 19. 25. A method for stimulating and/orexpanding T cells specific for a tumor protein, comprising contacting Tcells with at least one component selected from the group consisting of:(a) polypeptides according to claim 19; (b) polynucleotides according toclaim 18; and (c) antigen-presenting cells that express a polypeptideencoded by a polynucleotide according to claim 18, under conditions andfor a time sufficient to permit the stimulation and/or expansion of Tcells.
 26. An isolated T cell population, comprising T cells preparedaccording to the method of claim
 26. 27. A composition comprising afirst component selected from the group consisting of physiologicallyacceptable carriers and immunostimulants, and a second componentselected from the group consisting of: (a) polypeptides according toclaim 19; (b) polynucleotides according to claim 18; (c) antibodiesaccording to claim 22; (d) fusion proteins according to claim 24; (e) Tcell populations according to claim 27; and antigen presenting cellsthat express a polypeptide according to claim
 19. 28. A method forstimulating an immune response in a patient, comprising administering tothe patient a composition of claim
 28. 29. A method for the treatment ofa cancer in a patient, comprising administering to the patient acomposition of claim
 28. 30. A diagnostic kit comprising at least oneoligonucleotide according to claim
 25. 31. A diagnostic kit comprisingat least one antibody according to claim 22 and a detection reagent,wherein the detection reagent comprises a reporter group.
 32. A methodfor inhibiting the development of a cancer in a patient, comprising thesteps of: (a) incubating CD4+ and/or CD8+T cells isolated from a patientwith at least one component selected from the group consisting of: (i)polypeptides according to claim 19; (ii) polynucleotides according toclaim 18; and (iii) antigen presenting cells that express a polypeptideof claim 19, such that T cell proliferate; (b) administering to thepatient an effective amount of the proliferated T cells, and therebyinhibiting the development of a cancer in the patient.